Well, no. You have to distinguish between a clear and unchangeable teaching--that abortion is wrong because it always involves the taking of an innocent life--and a prudential judgment.
When it comes to war, there are only prudential judgments. All abortions are wrong. Some wars are wrong; some are right; some are a mixed bag. The Catholic Church has traditionally relied on just war theory to decide whether or not a war is justified. Among other things, this theory teaches that it is ultimately for the political leaders immediately concerned to decide whether a war is just or not. It is a prudential decision. War is never desirable, but sometimes it is necessary.
The Pope has never said outright that the war on terror was wrong. Some Vatican "spokesmen" have said as much, but they spoke out of turn and beyond their authority.