The means certainly exist to align two recorded tracks to within a small fraction of a single sampling interval--Cedar Audio's been doing this for years with 0.01 sample precision. But this capability isn't made available as such in conventional editing software. You'd have to take a somewhat roundabout route of upsampling, aligning, matrixing and then downsampling again.
Just taking 44.1 kHz for a moment--a one-sample timing discrepancy would equal an adjustment of between 1/3" and 1/4" in the relative distance of two microphones from the sound source. As far as I'm aware, sharpness of localization depends most of all on midrange and upper midrange timing relationships, so I'd be surprised if even finer corrections would often be needed.
On the other hand for M/S recording it's hard to imagine why it should ever be necessary to adjust by more than a tiny amount, even if that does give a sonic benefit--because it's just not that hard to get right in the first place. Last night I hung an M/S pair and by choosing appropriate mounting hardware, got the centers of the two capsules to align in the vertical plane within maybe 1/16"; I doubt that I'll have to time-slip those two channels any.
--best regards