I think this is rather silly of Paramount if that is their only reason. The bottom line is both of his last two movies, which were released around the time of the craziness, were blockbusters, to wit:
Mission Impossible III
TOTAL LIFETIME GROSSES
Domestic: $133,501,348 34.0%
+ Foreign: $259,660,663 66.0%
--------------------------------------
= Worldwide: $393,162,011
http://www.boxofficemojo.com/movies/?id=mi3.htm
and
War of the Worlds
TOTAL LIFETIME GROSSES
Domestic: $234,280,354 39.6%
+ Foreign: $357,459,025 60.4%
----------------------------------
= Worldwide: $591,739,379
http://www.boxofficemojo.com/movies/...ftheworlds.htm
So, he still is a bankable star.
I think Cruise and Wagnor wanted too much of the gross, which they certainly could command after the long string of successes and then these last two.
Note -- I make no comment on Cruise's antics. I am looking at this from a business aspect only.