the rachni queen has been shown capable of manipulating other species, who knows what it could've done with all of those dying asari commandos, also, if you left it in the cage, then contacted the council, they would have killed it, no questions asked.
Actually, I chose that background and was able to talk with the illusive man about it, he claimed to know nothing of the splinter group, and would have ordered miranda to kill them all if your buddy didn't do it in the first place, the cutscene is a little easy to miss, just antagonize the illusive man and you'll be talking about it.
Don't forget, the council have no idea how advanced the geth are, if you read the codex on ships you'll see they replicated sovreigns guns in less than two years, so it would not be hard to believe the geth couldn't create them, and the reaper artifacts you ffind they believe to be prothean, like the mass relays.
lastly, a lot of choices are black and white, or shades of gray phrased differently. For example, destroying the collector station, if you had an option to give it to the alliance, many of the highest ranking alliance members are pro cerberus, and cerburus could claim it was their discovery, if you tried giving it to the council, cerberus would claim it was a human find, and also theirs, not to mention, cerberus engineers are the only ones who know how to get to the station in the first place.