If you hadn't unlocked the controls, he would have died in there anyhow. He needed to live long enough for you to do it.
Still, your frustration is genuine- you do feel this mission could have certainly gone better.
You also feel a little confused, Vlad. Having now briefly met Balek, you believe everything everyone said about him being such a ruthless bastard. But... he's left your ship intact. He didn't set the station on self-destruct or anything. Frankly, he had you guys pretty well under his heel, but he chose to run instead.
In fact, that's only half the mystery. The other half is why Balek did it at all. This is Balek- the super careful, cunning killer who does not slip up. Even when Gundark had a bounty on her head enough to let him retire for life if he had gotten it, Balek never attacked her in Republican space. He trailed her, kept track of her, but he never did anything on the wrong side of the law. The only bounties he tried to take in Republican space were on Kuylen's men (from the Dark Side thread). He knew exactly what he could and could not do, and that is why you could nopt just arrest him years ago and get it over with. He waited for Gundark to leave the Republic before he took a shot of her, where the legality of it was not an issue.
But now? He just launched a vicious, murderous attack on three Jedi- and none of you even have a Bounty on you. His career is over. The Order will put a Galaxy wide manhunt on him. What the heck would persuade a man of Balek's careful nature to do something quite this monumentally reckless... and then cut and run?