First: I don't think you are wrong about this, because while I understand developing the new guy, there was also the fact that we did need to close on Green in particular (N-G). The decision to have Gerry lead this may have stemmed from the idea that it wasn't going to be a brutal recruitment against a powerhouse. We had no idea we'd be going up against Kentucky when it all started and I think the premise was that Green was a strong SU lean at the beginning. Add to that the fact that Hopkins was going to be unavailable due to US Basketball commitments all summer and I can see why Gerry got the call there. In hindsight, it may or may not have been a poor decision because there is not promise that Hop would have beat out Calipari either. I think what Hop might have been able to do was to get the commitment before Calipari even got his hooks into Green. We'll never know.
So then the question becomes: how smart was it for JB to invest both his own time and Hopkins' time into USA Basketball? Again in hindsight, it hurt the SU program in the short term because of their absence during crucial times. I'm sure the rationale was that it would substantively aid Hopkin's in two ways: street cred for recruiting and future coaching abilities. This was a great developmental opportunity for our future head coach. In that light, it was a good move, but since he left, clearly we got no benefit from it.
As to internal strife: I agree there must have been something very off about the Hopkins/Boeheim relationship or vision for the future. Hopkins leaving the way he did cannot be interpreted any other way. It was a very badly botched exercise in many ways. That, and not recruiting strategy, is the biggest flub that has happened in my opinion.