Maybe. PHD2 is pretty smart if it has an ASCOM connection to the mount. I know it will detect slewing and stop guiding (I don't know if it will start back up), I'm also not sure how it would handle a pier flip.
I'm not saying this is ideal. I'm saying this is a bug we need to address, but to work around it for the time being you may be able to deselect an auto guider.
I read your initial post wrong. I thought it was dithering but you didn't want it to. Sounds like we didn't command a dither but then waited for guiding to settle. That could be valid (but unlikely), I can't personally think of a reason why that would be a valid use but I'm sure some of our very creative users will prove me wrong 
Thanks,
Jared