How about providing the old class as backwards compatibility - but deprecated?

Maybe something like

     class SpaceTimeRealign(Realign4d):
        def __init__(self, desired_arguments....)

    @numpy.utils.deprecate("Please use SpaceTimeRealign instead")
    class FMRIRealign(SpaceTimeRealign):
        def __init__(self, old_arguments...)

That would be less painful.  For example - my students have current nipy - without this change they won't be able to run their slice time / motion correction scripts in the next version...