You're all working from the assumption that people who were synthesised suddenly woke up and were all like ' Man Shepard went and wiped out all diseases gave us near infinite knowledge and created galactic peace forever! And now we might even transcend death itself....what a dick.'
Playing a little bit of devil's advocate here:
I can see some of the galaxy thinking. "Gee, thanks for forcing a union between machine and organics. We appreciate our choices being completely removed from us."
Or, "Wow, now I can even crush my old enemies stronger thanks to this upgrade. Oh, I can recruit former Reaper creations to my cause? Thanks Shep!"
Also, can you imagine the horror of a Husk realizing what it's done? Say, this newfound synthesis also gives them memory. All the things they've done to others could come back, as well as the memories of getting killed and/or husked on top of it. This is highly unlikely, but it's still a thought I had.
As for "galactic peace forever," well there is a hitch to that. Mortal nature being what it is, eventually folks will find reasons to war with each other. Different cultures and societies still exist.
Also, while war time can bring peace, it very rarely fixes old hatreds for good. Not all krogan are going to want to surviving the war preventing their anger towards the salarians and turians from turning violent. The wrong people get into power after the war and it could spell real trouble. Not all of the mercs are going to go on to lead respectable lives after the war. There's been several planets that are just bombarded down to the ground, and are probably uninhabitable for some time after the war. All of the resources that the galaxy had were pretty much poured into that device and it's going to be hard going for most sorts of supplies for awhile.
War will happen again. It may not be in 10 years, it may not be in 200, but I really think it's bound it happen sooner or later. Sure, there won't be anymore war between synthetics and organics (which don't get me wrong, I think that's a great thing,) but to say there will be everlasting peace in the galaxy is a pretty big stretch.
Mind you, this is all in my opinion. I'm certainly not claiming to be any sort of expert on the series. It's just some various thoughts I've had bouncing around while playing ME3 this time. <shrug>