Points are added to your file (yes added, not deducted) when you are declared guilty, either through a guilty plea being entered in the file or by a judge declaring you guilty.
If you got the same ticket a few weeks ago, the points might not have been added yet if you still haven't sent in your payment and plea or if you just sent them in, there's probably an administrative delay.
Don't listen to the cop, if you pay this ticket now, your license will be revoke for 3 months, and when you get it back, you'll still have 2 points on it. The time to obtain your probationnary license will also be increased since the 3 months without a license do not count towards getting your real permit.
You don't have much choice at this point. Just contest it and when they call you, after you have your real permit, you can just change your plea and pay the ticket.