I think what happened here is you forgot to undo the MC_F whitening filter which is the Generic Pentek Interface board next to the MC servo board. I suggest you guys measure this on Monday so you can correctly estimate the MC length noise. And then perhaps undo the whitening in the anti-whitening filter of this filter bank so that the signal which is recorded is in units of kHz.
This should allow your online subtraction filter to be more correct: roughly speaking, the phase shift below a pole or zero is going to be 45*(f/fp) deg. Since we expect there to be 2 zeros at 15 Hz, it would be 9 deg phase shift at 1.5 Hz and limit the subtraction to ~80%.
While it is true that the whitening filter was incorrectly handled, I don't think this should change the subtraction performance since the MC_L data used for the Wiener filter training was also taken without undoing the whitening filter.