Just for the record, my son was on the USS Abraham Lincoln. They were returning from a 10 month assignment, the longest of any carrier. The sign in question WAS put up in recognition of the completion, finally, of their long mission.

i.e. this banner had nothing to do with Bush's announcement of the end of the war on the USS Lincoln, nor was this sign in recognition of his visit.

If anyone wants to know what is true, one can always contact the Navy. After reading the bulk of this discussion here however, it seems like 'what is true' isn't really of interest.