I would not to stop them. If you let them play such overpowered races then they'll expect a higher power game, artificially decreasing their power by canceling out all their cool abilities just takes the fun out of the game.
Instead of that just increase the number of opponents or their CR. For races with thirty points the Race Builder advises increasing CR by +2 in levels 1-5, +1 in levels 6-10, and by nothing after that. Take note of the template they took and add its CR to the CR of encounters as well. This formula won't be perfect, but you can fiddle around with the CRs until you find something appropriately challenging for your group.
I'd also advise making all the templates have equal CR adjustments, but if the game's already started the players will not like you taking away their stuff.