A Cruise representative denied the rumor, phrased in a way that may have been crafted to be literally true but misleading (a method frequently used by George W. Bush, as documented in the book All the President's Spin).
(Via Dispatches from the Culture Wars.)
UPDATE (March 18, 2006): Trey Parker and Matt Stone have declared war on Scientology:
Matt Stone and Trey Parker, creators of the animated satire, are digging in against the celebrity-endorsed religion after a controversial episode mocking outspoken Scientologist Tom Cruise was yanked abruptly from the schedule Wednesday - with Internet rumors it was covert warfare by Cruise that led to its departure.
"So, Scientology, you may have won THIS battle, but the million-year war for earth has just begun!" the "South Park" creators said in a statement Friday in Daily Variety. "Temporarily anozinizing our episode will NOT stop us from keeping Thetans forever trapped in your pitiful man-bodies... You have obstructed us for now, but your feeble bid to save humanity will fail!"