I often book hotel rooms for friends who are visiting, and in such cases I've earned points even though the friend used his own credit card to pay. But then, these aren't people who have their own hotel membership nor care.

In the OP's case, I suggest a quiet and friendly word with the boss, to see how strongly he feels about the issue; it may be that the boss likes the points but doesn't mind too much if the OP gets them, or it might be a fight to the death and the OP would need to ask himself if this issue is worth his job.