Yeah I'm waiting for the continuation as well. Should be fun.
As for the stun setting, um yeah. I was like "Stun? I like killin' Well, ok then." They did work around that bit in a good way I thought by having the NPCs go "dizzy" or dazed, just short of blowing them away, lol.
Yeah, I'm also excited for the continuation - I hope that it splits into 2 paths.
The level of trust that Section 31 would have for you would differ dependant on the actions chosen in the initial confrontation and thusly with which missions they would entrust you with.