They're pretty clear in their terms and conditions, and always have been. (Starwood was, too.)

Regular travel agent-booked stays do count for status and earn benefits, but "online" travel agent and consolidator stays (Priceline, Hotels.com, etc, etc.) never have.

Marriott isn't stripping you of anything. If anyone's to blame, it's your employer and their travel agent -- not Marriott.

Our corporate travel agent (which we're required to use) has access to hotel rates from a variety of sources -- including some of the online TAs and consolidators like Hotels.com. I tell them not to book those rates, and instruct them to book 'regular' Marriott rates instead. That always works for me.