The organization as a whole, primarily upstairs, isn't exactly a bedrock of honesty and candidness, but I think that often gets more credit than it's due. That said Paul Allen and Larry Miller are not particularly likeable folks.
I have little doubt that there's some truth to Ziegler's accusations, but to think Portland wasn't considering the long-game in dealing with Roy's knees seems silly. Was he rushed back on demand of management for the 2011 playoffs? Hard to say. But it would be unspeakably foolish for an organization a year into a max contract to rush the star player back at peril of his future.
Allen and Miller have made some tremendously stupid moves, usually from a PR standpoint, but the team was built around Roy, to the point of input in moves, and that amount of influence and respect leave it hard for me to believe he wanted to leave town so badly as to retire.