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.
Real Programmers don't write in FORTRAN. FORTRAN is for pipe stress freaks and crystallography weenies. FORTRAN is for wimp engineers who wear white socks.