This is why the laser is split, and sent down two perpendicular paths. Sure, a wave might stretch the spacetime of the X axis... but that same stretching wouldn't effect a similar increase in the return time of the Y axis. This very stretching of the measuring device itself against one axis(thus modifying the round-trip time of the split laser as compared to a perpendicular path) is the very thing that they are measuring.
Your pet theory, and their experiment, match.
We all agree on the necessity of compromise. We just can't agree on when it's necessary to compromise. -- Larry Wall