Assume. Lets break it down. Ass. U. Me.
Assume makes an ass of you and me.

There's no way the base won't have indoctrinators aboard.
Sovereign was never designed to be piloted by little aliens, either, and he was full of Indoctrination.
Besides... Cerberus? Good guys? Taking over?
I'm all for using resources where they're available, but Cerberus are still the guys who ran the experiments on Jack, no matter what Miss PR Lawson says. They still throw Alliance marines at random alien fauna, then kidnap the survivors for experiments. They still create Creepers and Rachni and god-damn
Husks and other gribbly monsters to unleash upon unsuspecting aliens and any humans who don't agree with them. You thought the cosmetics companies were bad for testing on pigs? They've got nothing on Cerberus.
Keeping the base was a bad idea from any angle. This;
Anacronian Stryx wrote...
I think Cerberus will be after Shep no matter what.
Keep the base = Indoctrinated Cerberus.
Blow up the base = Shep destroyed the best hope for humanity(in TIM views) plus he/she knows to much about Cerberus to be kept alive.
pretty much sums it up. If you keep the base, either Cerberus switch to Team Harbinger, or Cerberus (the EVIL MAFIA) take over everything.