Well my point with the lesser of two evils idea is that Palpatine didn't just kill everything he saw, like the Vong did, so while his regime was corrupt as hell, they were a hell of a lot better than the Vong, and if they weren't destroyed, the Vong would have never showed up. I'm not too familiar with what Nom Anor did to help the Rebellion. However, it would have saved those 365 trillion lives.
Comparing the Vong and Palpatine is hard to do; the Vong did what they did because they were warriors. They're the SW version of the Spartins. Hell, they were just following the orders of a megalomaniac (Shimrra). On the other hand, Palpatine manipulated, tortured, and murdered for his own benefit, on pure ambition, and as the DSSB says "to squeeze the life out of the galaxy that spawned him" like a cloaked parasite.
But, yes, you have a point. Palpatine didn't butcher senselessly as long as people did what they were told, whereas the Vong had this hatred for all non-Vong things.
Nom Anor was up to his balls in subterfuge involving the Empire. He helped facilitate numerous betrayals and warlords, which, as you know, depleted the Imperial Starfleet and the Imperial military's reserves and weaponry. Anor was well aware that a unified Empire would curbstomp the Yuuzhan Vong, as did Grand Admiral Thrawn, which was why he tried to help the Empire. The truth was: Thrawn had no real love for the Emperor or the Empire as a whole, but understood that they stood the best chance to protect the galaxy from the Vong.
I am familiar with a little bit of what Palpatine knew about the Vong. Correct me if I'm wrong but didn't Anakin and Obiwan travel to Zenoma Sekot? And I'm assuming they reported their findings of "Extra galactic" species to Palpatine? I wonder if was too arrogant to believe it. Furthermore, didn't the prophets of the dark side warn him of these travelers?
All right. There was a Republic project called "Outbound Flight" led by Jorus C'Boath during Palpatine's tenure as Chancellor [before the Separatist crisis]. C'Boath was a Dooku-type Jedi, arrogant and proud, and wished to expand the Republic and the Jedi Order to the far reaches of the galaxy, the Unknown Regions.
However, Darth Sidious was well aware of the Yuuzhan Vong scouts active in the Unknown Regions. We're never told how he found out, but Palpatine is usually ten steps ahead of everyone as far as information is concerned.
Anyways, Palpatine reasons: if Outbound Flight makes it to the Unknown Regions, they could bump into the Vong invasion force. And if that happens, C'Boath would likely get captured and the Vong would have prisoners to interrogate. But more importantly, if that happened, the Republic would be screwed, since - at this time - they had no standing military force.
...So, when Outbound Flight takes off, Sidious sends a Trade Federation mini-fleet to intercept it and destroy it. However, before he can, a Chiss striketeam intercepts them and WTFpwns them (despite having vastly inferior weaponry). Who is leading this Chiss strike team...
Effin' Thrawn.
One of Palpatine's agents who survived the Chiss attack, Kinman Doriana, persuades Thrawn to destroy Outbound Flight, and puts Thrawn in contact with Sidious. Sidious tells him the reasons why he tried to destroy Outbound Flight, so that he [Sidious] would have time to prepare a military strong enough to stop the Vong [the Empire].
Long story short, Thrawn curbstomps Outbound Flight, and Sidious secretly has C'Boath cloned into the insane Dark Jedi we all know and love from the Heir to the Empire trilogy: Joruus C'Boath.
Whew.
Anyways, we know that Palpatine obviously didn't create the Empire to just stop the Vong, but it was one of the reasons why he put so much emphasis on the military, hence why Thrawn later signed up with him.