Side ops not being rated are great in that it actually gave me a reason to kill and use the other 95% of weapons in the game like you mentioned. But, that still doesn't change the fact I'm doing the same 5 or so mission types in a viage I ha e already been through 4 times.
I doubt reviewers had time to touch any sideop that wasn't yellow
You don't get penalized for using lethal weapons in the scoring system. You miss out on a 5000 point bonus for no kills, but in a lot of missions speed gives you the biggest bonus. I've certainly gotten S ranks while playing "loud."