Honestly, I think the more troubling sign (not the punt return fumble) for Harper is that the Pats specifically gameplanned to keep him off the field on offense. I don't know when exactly his first snap was, but I'm pretty sure we saw formations with seven offensive linemen, three tight ends, or two running backs before Harper made it on the field as the third WR.
Obviously we won't write off his entire future right now, but he's destined for a trip back to the practice squad. I would have expected him to stick on the roster as the #4 until both Edelman and Amendola are back, but after tonight I wonder if they cut him once Amendola is healthy. It's hardly worth having Harper on the roster as the #4 if they refuse to use him even when he's the #3.
Edit: according to PFF_NateJahnke, Harper didn't see the field until the last minute of regulation, finishing with 5 snaps.