Yeah, so no matter what he'd have a skin-tight costume to wear. But even then, a lot of SHIELD agents would have to use lethal force sometimes, even Captain America and Black Widow, though they go to length to avoid it.
Hmm... if Peter was in SHIELD he'd probably hang out and work with Black Widow a lot... Peter/Natasha?
Now that I think of it, I think there was a What If where Peter ended up in SHIELD, though I forget how. I think he had kind of a Deadpool-ish costume. I'll have to go look it up.