I think Morey sees it the other way. Ben is the best player the Nets can get for Harden and if they don't do it now, the throw-ins won't be as good in July. And/or Harden could opt-out and the Sixers would just sign him (they have to move Tobias to do that, but would presumably find a way).
That hurts the Sixers this season, but the Nets know he's already willing to hold on to Ben and do that for a better long-term situation (in many ways).
Meanwhile, the Nets could still win it all this year if they keep Harden, but not if he's slacking/distracting.
Whatever's going on and whatever happens, there's no question Morey loves the guy a bit too much, but he didn't cave to Houston either.