Sometimes travel agents have access to special low rates that are not available to the general public, or negotiated corporate rates that are lower than any published rate. You may have gotten such a rate. If that's the reason, you or your employer surely saved more than the points are worth. (If your travel is paid for by someone else, they have a right to set reasonable conditions for it. Whether or not your employer's conditions are reasonable would be off-topic for this thread.) If you are willing to pay the difference out of your own pocket, perhaps because you want stay credit toward status, there may be a way for your corporate TA to book a rate that earns credit in the chain's frequent guest program and charge you the difference. You may be unpleasantly surprised at how much that difference is, though. It would not be ethical to ask your company to foot the bill for your status unless you own the company.
Also, check the terms and conditions of the chain's frequent guest program to see if it says anything about rooms booked by travel agents or other third parties. If those bookings don't earn credit, your only option (if you want credit) is to book another way - if that's possible in your situation. Unless you're very senior or irreplaceable, it may not be.