Certainly they made up, because they are best friends/comrades in arms/partners in crime/like siblings and parent , and whatever other description that you might care to use. Given the life style that they had adopted, liking and trusting the person who might have your back at a crucial moment is a simple matter of self preservation.
I do think, however, that this was the point in their mutual friendship when each of them began to see, for the first time since Buffy had come to Sunnydale, themselves more as individuals than they had done previously, and come to the realization that having their own separate lives in no way weakened their effectiveness as a team or the depth of their friendship.
I'm in no way defending what Spike tried to do, but it did serve that one useful purpose.