A bigger war crime? Surely not. A city and a few casualties are a small consequence compared to the destruction of one's planet. Sure, the Atlanteans have now been left homeless and displaced, and are almost certainly full of feelings of hatred and resentment towards the surface world. Understandably so. With that said, in their current state they are little threat to the surface, and even if Atlantean justice were to be dealt out upon the world there are more than enough heroes capable of quelling such attacks. Besides, there are other members of the royal family out there capable of leading the Atlanteans away from violent action; a path (considering their already tentative relationship with the surface world) that is in their own best interest.
Now, concerning the fallen king. Let's not pretend Namor was much more than a narcissistic, arrogant and self-serving opportunist whom played whatever part made him look better or suited his agenda and people best. He was however a decent monarch and to a broader extent - character, one whose absence will be felt. However, he was the architect of his own undoing. You don't get to walk away scot-free from the kind of actions he took while with the Illuminati and Cabal. Let's not forget his hypocrisy in the first issue of the Squadron Supreme alone either. He has the audacity to suggest that their action against Atlantis was little more than base revenge yet when Hyperion wrecks Atlantis, Namor in turn shows his true colors when he is overcome by rage and murderous intent, seeking revenge for his and his people's loss, which is somehow justified in his mind. Yet, he thinks them mad. Too bad he is cut short...
Namor took it upon himself to act as judge, jury and executioner. He judged that destroying someone else's planet to save his own was the lesser of two evils, he decided his actions were necessary and then he pressed the button. He played god and paid a hefty price. It isn't very pleasant when the tables are turned. He was judged in much the same manner and as a result he suffered a very similar fate, one which he saw himself fit to press upon others. At least his people were given a chance. They may be homeless and without a king but they still have their lives. Countless opportunities remain for them. The oceans are vast and filled with riches - they can rebuild. Their hope has not been extinguished. Namor on the other hand, didn't show the same clemency to the people of Doctor Spectrum's world.
At this point, having made their intentions astoundingly clear, reasoning with the team would be futile. Perhaps if Thor were around he could talk Hyperion down, which would affect the team's dynamic dramatically and diminish their firepower drastically, and maybe even end their crusade much quicker and with less bloodshed but aside from that I don't see how this doesn't end in some sort of calamity.
Currently, I don't believe there are many heroes/teams residing on Earth-616 that have what it takes to put down/away such a determined and powerful team. Hyperion's potential alone makes him a beast on his own, even if he's lacking combat feats, but when you pair that with a roster of equally dangerous people (albeit in very different ways) at his side, it makes for a formidable adversary. Focusing just on the most obvious threat - Hyperion, there are very few who can contend with him. Two of the most obvious and go-to choices are: Hulk (Cho) whom has too little experience, and the current Thor whom has done very little to convince me she could do much more than hold him off for a period of time.
The Ultimates are a formidable team in their own right. Black Panther's intelligence and resources, Spectrum's speed, Captain Marvel's experience and Binary powers, Ms. America's ambiguous yet seemingly impressive powers and finally Blue Marvel's own impressive intellect and powers which affords him at least peer status to Hyperion are not to be taken lightly. Blue Marvel is obviously the biggest threat on the team, having fought versions of Hyperion already, he's proven he can hang. However, this particular Hyperion has been consistently depicted from his very first appearance as arguably the strongest incarnation of the character yet. So yes, Blue Marvel has fought a Hyperion or two before, but he hasn't scuffled with this guy before.
Jim/Steve's Avenger team on the other hand, are rife with experience but certainly lacking the brute-force necessary to physically engage with the SS on even terms. Rogue stands the best chance, but with the Squadron's level of monitoring they would surely be aware of her powers and have countermeasures should they need to deal with her. An aged Steve, even with all his experience poses little threat, Synapse is still too green and very little is known about her, Deadpool is basically a non-factor, Jim doesn't have the damage output to hurt Hyperion in any significant way, Quicksilver might have a speed advantage considering his fluctuating speed levels and Hyperion's ill-defined speed and finally Doctor Voodoo presents a significant variable as this Hyperion hasn't really dealt with magic.
Other teams like the X-Men probably wouldn't want to paint a target on their back considering their track record of being hunted down for one reason or another. They already have enough enemies. The New Avengers sans Squirrel Girl and her obvious hax just don't cut it. The ANADA are an equally new team but this team consists of a few comparatively inexperienced teenagers. Tony's a wildcard with his ever-evolving armor and Nova's been pushed quite a bit lately in terms of power but the rest minus Thor aren't stacking up to a serious Hyperion. This is obviously all speculation and based on my opinions but this is how I perceive how these heroes/teams would fare. Now with that in mind, none of this is taking the other Squadron members into account. With them it's pretty much a whole different story. I'll give you that Wakanda and the Cabal are probably too much for the Squadron as is, in regards to their current tactics.
It's my opinion that to beat a team as resolute and unhesitating as this, the others would have to combine forces and pool their resources given the downsized nature of the current teams, both in numbers and seemingly overall power. Not to mention that the majority of these teams are also new and still learning to be competent as a whole. A good plan and overwhelming numbers could do the job but probably not without significant casualties.
Lastly it irks me how quick the other heroes are to judge. Very few of them have experienced this kind of loss. They now see villains (or just shy from it) in place of heroes, but really they are just misguided. They're like orphans clinging to any semblance of belonging and safety, doing whatever they have to to ensure that what little they have isn't taken from them again. Some of these characters are known to be great heroes. Hyperion for example has proven himself an honorable man with a deep understanding of moral and philosophical ideologies and has put these very ideals to the test. He doesn't take life lightly and is more than willing to sacrifice himself for the greater good. He did so just recently before being brought back along with Earth-616. It seems this one action overrides all the heroic deeds he's done in the name of his new home. Next, imagine how traumatizing it must have been for Doctor Spectrum for her to become like this. She comes from a world where a utopia wasn't a pipe dream but little more than hop, skip and jump away. She was a part of a team who wouldn't even consider the things the Illuminati did, even though her team and world were facing the same desperate situation. Meanwhile the other former Illuminati members and their contributions to what happened are overlooked by their peers. Perhaps it's because they are such prominent people; long standing heroes with good reputations as such. It might just be more convenient to let let it slide and forget. Who knows. They are always preaching accountability but many are just hypocrites.
The Squadron Supreme's actions, good or bad, justified or not, will be entertaining to see play out at the very least.