Because he was massively abused as a kid to do it. Mentally, emotionally, physically, and magically tortured because he had a tie to the sword. His nature is not violent. 
Outright he could kill her. But he is hesitating to since he is no longer forced/required too and wants away from it.

he basically does. They don't do what he is wanting though. His goal is to purify the souls the dragon stole not destroy them.

He mentions when testing they don't act like old 12lb did. That they are firing different

Was obvious this was going to be a theme from the get go. He literally says "I can't get past this level so I can't learn new skills" in the first few chapters. Like, this is a plot point.

He is HIDING so he doesn't get hunted down, tortured, and worse, those around him get brutalized. It's the current plot. . .

Remember that ancient story. 
That's the issue. He isn't worried for himself. It's others he is terrified for.

pretty common troupe. Most likely accurate. The church probably hates them due to either 1 killing someone, 1 losing control (the demons bite) and killing others, or simply because they cant control them/own them

he was planning to go camping and had all of it in his bag, but got forced to the fireworks

if it was reverse, in manga, it would be normal.