You are assuming that nothing around Harry changes, that all the people around him remain the same.. That's the mistake I think, because Harry's choice and his change in this other universe doesn't happen in a vacuum.
No, I agree: things around Harry
will begin changing, from the moment of "the Choice."
Harry changes, so what Harry does changes -- how he acts, how he reacts -- and everyone in his orbit will in turn be changed.
But Michael's northstar isn't Harry; it never was. He'll be among the less-changed (at least for the first few books); I don't expect any of Harry's changes will affect Michael's faith, or status as a Knight, or his Divine Guidance to help others in need.
And because there is a confluence in Chicago -- all of the same "dark powers" that Harry noted are still coming to bear, there -- I think Michael will more-often be Guided to Murphy's aid, than he originally was in the first few books.