Not necessarily. If Bush doesn't step in and stop this killing of Lott, the Republicans will walk away much weaker than they are and he will not see much, if any, of his proposals being passed.
Bush should do the right thing and affirm his support for Lott, who has unabashedly supported the president in supporting his legislation.
Bush cannot "affirm" something that isn't so, therefore it would be the wrong thing to do---to say he supports Lott when he does not.