I wouldn't have gone for this. If he screwed up, he screwed up, and should have torn it out. I don't trust the situation, and any tile setter worth his salt wouldn't have installed a second layer over the first in the first place, so any tile setter who would probably didn't take the time to make sure the surface was good, nor did he prep the first layer of tile to make sure the thin set for the second layer would adhere. My guess is your second layer will start coming loose in about 18 months or less.
This of course is not to mention the fact that your bathroom floor is now higher than the hall carpet and presents a trip hazard.
As a general contractor and a homeowner, I would make the tile guy rip the tile out down to the backerboard, and if he can't get a clean layer of backerboard, replace that too. This was HIS screw up, not yours, and YOU are the one who has to live with the results, not him. Heck, as the saying goes, "I can't see it from my house!" and neither can he.