The terms of the contract with the conference will determine if points/stay credit are allowed or not. Often the contract may include certain hotel services (breakout rooms, food, beverages) based upon attendees paying a higher rate. This can reduce or eliminate conference registration fees.

Check with the conference organizers to see if this is the case. If it isn't and the hotel insists it is, maybe a different property is in order for future business. Knowing ahead may help you determine if you should book the conference rate (although they may do a name match) or even stay at the same property.