Here's the thing: If the Jets had made the move to fire MacCagnan immediately after the draft then certain Eagles staffers who had their contract expire could have held off on signing extensions and/or the Eagles could have made inquiries with other personnel types around the league whose contract was up about their interest in joining the Eagles' staff. The Jets waited so long though that almost all of the Eagles' staffers are under contract and so are most of the personnel types around the league so the Eagles' external options for replacing guys like Weidl or Ian Cunningham would be very limited if they let them leave to join the Jets. Now the best thing for the Eagles is to promote internally. They have a pipeline ready so that Weidl can replace Douglas. Ian Cunningham will likely get bumped to asst dir of player personnel and then in a year or two may be ready to be bumped to Weidl's spot if Weidl gets a GM job elsewhere. The Eagles are already losing a key guy in Douglas, I don't think it's reasonable to expect them to let multiple front office guys leave at this point in the offseason. Those guys will be taken care of with promotions/raises.
As far as other situations, I assume you're referring to DeFelippo. I'd agree that ideally you don't want to block a guy from receiving a promotion. However, Wentz was in his 2nd year and his development trumped all. The Eagles hadn't had the same QBs coach for more than a year since 2012. I can see the team wanting a little stability there. Besides, that was an owner call. Roseman and Pederson were willing to let DeFelippo leave but got overruled. Can't complain about how it worked out.