By then, yeah I think he thought so too (which isn't an excuse by any means, because being "in over your head" is a bullshit excuse unless you think it'll cause even more deaths — it just makes the scene a lot sadder). But if he hadn't opened the portal and decided to screw over the Chitauri and tell Thor everything on the Helicarrier, he still could've found a way to get the hell out of there without causing the deaths of loads of people, and then worried about hiding from the chitauri because, you know, innocent people first, guy who almost tried to conquer them all second. So I can't really bring myself to sympathize with his regret.