It's very probably a coincidence. Music rights have become something of a problem in the last few years, which just happens to coincide with Disney's acquisition of the Muppets. It's entirely probable that Columbia would have hit the same problem had they been able to continue with their releases.
Basically, it boils down to this: the rights-holder is under no obligation to license the use of their property to anyone. If they choose to do so, they can choose what - if anything - they want to charge for it. The situation changes all the time as the perceived value of a particular recording alters. For example, it is not currently possible to license original Beatles recordings for home video use. This is a fairly recent change - a few years ago, it was fine. It also varies by country: all four seasons of Quantum Leap released to date have cuts in the US releases due to music problems; only the fourth season has been cut in the UK.
This isn't entirely a recent problem, however: MFC has never been available uncut in the US due to music rights issues.