I did that a few times. For instance, when Fran was searching for a way out of the prison I set her as the party leader just because in the actual storyline she knew where she was going. Oh, I'm so lame.
For the part with the alarm I just ran my ass off, used terminals, and then ran some more. I got out with only a few hits on me. And the boss battle was easy, just Fulminating Darkness with Basch and Feral Assault (or whatever) with Fran and he had like 1/3 of his HP left.