Well there are quite a few issues going on here.

First, you tell us that your company prepays your hotel, but your email to them states they sometimes pay your hotel. On the stays where you are paying for the room you should be getting the points and the stay credit.

Regarding the times when your company pays for the hotel on a direct bill, then by MR T&C they are not obligated to give you points or stay credits.

Have you spoken to your company about this? If you are traveling this much then your company should at least be able to set you up with status through their corporate contract with Marriott. You may also want to discuss with them the fact that it is your butt that is on the road all the time and that you would like the benefits that come with that sacrifice (points AND stay credit).

As an outsider looking in, I see your issue being more with your employer than with Marriott as Marriott is just honoring their own T&C the the terms they negotiated with your employer. Now if your company is paying you a salary well in excess of the norm, which would make up for this loss of this benefit, then no harm no foul. However, if they are not, then I would start looking for employment elsewhere if you can't come to some understanding with them or can't accept the situation the way it is.