There is probably a point at which increasing his distribution would negatively affect his FG%, but I doubt you’re close to that point with him, especially in triangle, which many observe lets you get away with higher distribution at the top, ie less penalty for high distribution players relative to the other sets. What hurts Duffy more than anything (at first glance, without digging into your pbps) is your team’s lack of perimeter shooting. Teams can go negative against you, and double him (especially if he’s not on the floor with your 2 guys who are at least some semblance of a perimeter threat). Not having a good distributor on the bench also hurts him significantly.
FT shooting is not insignificant, but at C- you’re looking at around 64%. The difference between that and B (~76%) is going to be around 20 points at the line over the course of a season, so less than a point per game, on average. Again, not insignificant, but I think you’re giving that too much weight in your decision making, especially for triangle. It looks like you’re trying to play a more FB/motion style offense. That’s a valid choice, just understand that you’re not getting as much from Duffy and A.Williams as you should be in a set that should utilize their skills nicely.