It affects the ending and makes it impossible to get the "best" one. Click the spoiler if you want to know why:
At the end of the Strike Force missions you assassinate Chairman Zhao, allowing the U.S. and China to become allied. If this isn't done, then there is no way to save the U.S.S. Obama from destruction. If you don't know why that affects the ending, then I won't spoil that for you.