That's why green is the problem. Neither synthetics or organics have a choice at all. The galaxy as a whole is subject to an extremely totalitarian whim.
If you pick control, nobody has to accept the reapers they can keep fighting against them as they have done before. The choice still exists in Control.
It's also worthwhile noting that in a merger between both organics and synthetics I'm not sure how much free will either would have left. In Red, Sheps decision could and would be subject to review by historians because the species more or less remain free and whole. In control the same thing applies. In synthesis it's not clear how much of the individual identities of either synthetics or organics remain and it's not clear if "freewill" will remain exactly that. I would suggest to you that in Synthesis Sheps decision will not be subject to any review as it would in the other two as you would normally do in free and democratic societies. That's really the key about synthesis. It changes how people are without their consensus. Control doesn't do that and Red only kills organics. It doesn't fundamentally alter them and make them different people.