I'm surprised this hasn't come up before - are you certain this hasn't been addressed in a prior season? If you can find an instance where this was scored one way or the other, that'll serve as a precedent and you don't have to figure it out.
Personally, every league I've played in scores KR or PR TDs to the individual player, not the team D. In other words, Defenses are strictly D, not special teams. The problem is, you can't do this in your league for this season, b/c teams already drafted Ds based upon special teams return potential, as well as D. So, you'll probably have to allow the "double dip" on the return TD, but start a discussion that resolves the issue one way or the other for next year. Not allowing double-dipping is a lot cleaner, IMO.