I pesonally didn't trust The Elusive Man. So I blow the shit of that base with my crue intact without remorse or doubt about what was next because I did a lot of missions putting Cerberus first in front of my decisions against the Alliances matters. Plus that Fucker set me up tons of time. There was something about those eyes, give me the chills. What I saw in that base was one of the reason on why I decided to destroy the the base, that monstr made out of humans beside giving the base could've backfired giving the fact that the Reapers are coming and You didn't really knows if that base was going to be re-taken with the rest of that abomination. Anyways one less enemy base is fine with me. Besides, destroying the Collectors base would be good in the eyes of the Alliance and for ME3 you'll need back up and I think.
You tell me.