I like how Bioware gave us a morally ambiguous choice, just like with the Rachni in ME 1, but am I the only one that thought the decision was a no-brainer? Think about it for a minute. Every single time anyone has ever tried to use Reaper technology, it's backfired horribly. Either the scientists were driven insane, or they awakened something that should have stayed asleep. No exceptions!
And because Collector technology is Prothean technology, and because Prothean technology is Reaper technology, you can't really say that since it's Collector technology it's not like they're stripping apart a dead Reaper for spare parts.
Plus scientists in video games are pros when it comes to screwing things up. Just look at Prototype, or the scientists at the beginning of Half-Life 1.
You really trust Mass Effect scientists- nay, the scientists belonging to a self-admitted human supremacist organization that's made some serious screw-ups in the past- to analyze the most dangerous technology in the universe? I think not. And even if it turns out the Collector technology's harmless, why hand it over to Cerberus?
Doesn't matter how alluring the Illusive Man's voice is, Cerberus cannot be trusted implictly under any circumstances. Even if everything works perfectly, you'll be giving a human supremacist organization the biggest boon they've ever received.
Besides, if you saved the Rachni queen, made nice with Legion, and rewrote the heretic Geth to rejoin Legion's geth, you should have more than enough allies for ME 3. And if not, I recommend destroying the base anyway, as Bioware wouldn't have made a choice where, if you chose the 'wrong' choice, you'd suffer for it in ME 3.