You are right that there should be some stragglers left behind. The game seems to support the idea that everyon left and the Geth stopped, which would be a remarkable feat. Well the story stuff surrounding the quarians is of such a "quality," you could consider killing the quarians at Rannoch as an act of mercy, so they don´t have to endure it any longer.
I thought your initial idea was that the major cities got nuked?
Were the liveships actually a thing back then. There is no need to grow food in space, when you have planets in resupply distance. OTOH I doubt that the quarians were able to erect temporary construction sites that could build them, so could be.
So now they sniped everyone leaving the planet? This makes it better how? They weren´t nuking a defenseless population way past after they were unable to fight back, now they are sniping people fleeing?
The codex lists a classification of WMD´s and how hard you violate council rules by type. uranium and plutonium aren´t rare, but the problem isn´t insufficent resources, but missing infrastructure. The galaxy moved beyond fission and it´s a good question if that stuff is still mined somewhere. Seems that some people are still building nukes. Turians and Krogans back in the day, probably loved them, but did the quarians mine and refine it? So it´s not so unlikely that the geth had to build the whole system from scratch.
Machinery isn´t necessarily immune to radiation. Electronic components have to be hardened specifically. Well, it´s the future, so could be different. I am not so well versed in that matter, perhaps someone more knowledgeable would like to elaborate?.