A plumber can bore out the hub to accept a new, longer riser with a ram-bit. Then she would fit a fairly long riser stub and leave that capped while you do your floor. When everything's done, she comes back and cuts the riser to the proper level and fits a new flange over the floor. That's more or less what I did on my recent tile job -- though I fit the flange at the end myself.
Another option could be to use flange extenders to get the flange to the height you want. 1-1/4 is a lot of extending, IMO.