The Council is BAD

Not all the Geth accepted the offer. Most did, but not all. Those who didn't were shackled, as we see when we encounter Legion or the Geth VI on the Geth Dreadnought. 

The Harvest is a slow process but it is also done in a galaxy in which none of the Mass Relays work for anybody but the Reapers. Every star cluster and solar system is cut off. Galactic society is over. That's what the Reapers do. They enter through the Citadel Mass Relay and capture the station. They then data-mine it for information and use it to turn off all the mass relays. Then they can take their time harvesting each isolated region without having to worry about a galactic response because a galactic community is impossible without the mass relays. That's what I mean when I say the stakes with Sovereign are as high as they are in the Reaper War itself in ME3. If you fail to stop Sovereign then the Reapers win the war here and now. The rest is just clean-up.

I would imagine it has something to do with the idea that the geth are supposed to be relatively resistant to hacking since they are a collection of many processes, so eventually some will correct. Also in ME1, Sovereign's ability to directly control entities seems to be somewhat limited, especially at range. All in all, I think it fits with what Legion tells you in ME2. Namely that the geth admire the "technological perfection" of the Reapers to an extent, but were not united in deciding to cooperate with them.

I don't know the best way to characterize the worship like reverence that is seen in ME1, at least on Feros. Kind of odd that it was in there at all, and probably isn't really a result of Sovereign's control given Saren's dialogue about how he finds it insulting (or something like that, can't recall the exact quote off hand).