1 CH characters killed on sight in inner VC = another reason for an alt, actually there're already alts, if only you're doc3 with 1 CH, so you'll need to eat mentats or drink beer each time you're entering a town.
For encouners, Enclave farming starts in TB by one guy who found them, then alot cripplers coming into encounter and making enclave invalids who fight unarmed, 1 CH or 10 CH it doesn't matter, simply that guy, who found them, will need to have >1 CH by eating mentats or drinking beer, or making special alt for this. The same about BoS, if you're going to farm them.
Also why you don't like 1 CH characters so much? It's just useless SPECIAL, it's ok that all non-merc-leaders have 1 CH.
Even if you'll force everyone to use >1 CH, then everyone will have to eat mentats and beer 24/7 to avoid whatever bad will happen to them, if it's really something bad. If it's only inner VC and enclave troopers, then noone will care about it, as I said above. Inner town need only for docs, they will have >1 CH or eat mentats/beer, encounters starting in TB ready and troopers waiting stupidly until cripplers start.