"How many evil overlords have you overthrown, now?" Shepard's question is rhetorical; she doesn't care for his methods. It's not the pettiness, Shepard knows well the pleasure of being petty to those who annoy you, and isn't shy about hurting people she deems worth the effort. It's that she's not convinced of what matters most: his efficacy.

But that's a discussion for another day. After all, you can't win the game unless you're willing to put a little in the pot.

"Yeah, alright. It'll kill time if nothing else: I'm in. On one condition."