I actually have implemented two things that work in that direction.
I only persist the employee if there has been a change and I also overrode the update_user method to only update the user if a change has actually occurred in the related fields.
This will work 90% of the time, except for the first sync for example. Also, my fear is that some cross company change someday will affect a field in all the employees and thus require the update to run for the complete Set.