Here is my understanding or the procedure (and how it has always applied to me).
If you either volunteer or are re-routed because of a mechanical or weather delay on a different NW or code share partner flight you are eligible for the miles flown.
If you are re-routed onto NON-partner airlines than you are eligible for the original itinerary earned in your NW account PLUS you are elligible to earn miles with the program of the carrier you are re-routed on (or one of their partner programs ie. US/UA).
I have never had the pleasure (dis-pleasure) of being re-routed on two seperate airlines for the same flight.
I would think if you have them remove the CO miles from IAH-MIA than they will credit you with the original miles of the itinerary and you can also earn miles with AA/Alaska or one of AA's partners for that section if you take it up with AA.