Sovereign was never "deactivated." Sovereign had been watching civilization progress and acting against it/to facilitate the purge. When you talk to the Rachni queen on Noveria, she tells that their entire race, who communicate telepathically, were indoctrinated (all our songs were drown out by a sour note from space) and made to fight the Rachni War. Sovereign knows about the Ilos relay being in Rachni space, because Sovereign had indoctrinated the rachni in the first place.
Failing that... You see sovereign active and hostile in the very first mission, and the conversation with Vigil at the end confirms that the keepers were "hacked" and didn't respond to the Citadel relay code. Saren (controlled by sovereign) shoots keepers out of fustration on the way to manual override, showing anger that it already tried to open the citadel remotely and failed.
ME2: Making the human reaper was trying to get a jump start on the war. If Sovereign was unable to storm the citadel with the geth fleet, I don't think they'd just throw one newborn reaper at it and hope for the best. What they needed was someone who understood us and could think like us. The events in Arrival show that the reapers were after the Alpha relay... basically an underground tunnel into the heart of the relay network. When Shepard destroyed it, they were forced into a very long "ground march" through Batarian space, which bought everyone else more time.
Ninja'd. Where did anything say the reapers were "inactive"? This comes up a lot... enough that I'm wondering if I missed something somewhere, despite playing all the games 3 or 4 times each. What I wrote above is (AFAIK) canon and the first two paragraphs all come from the first game, so there was no writing change. I tried to limit my argument to ME1 for that reason.