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.
The trouble with being punctual is that people think you have nothing more important to do.