Did you end up making yoghurt with this, and how did it go? I have a couple of bottles of goats milk in the freezer for some feta, as a bit of a test to see how well it works. We've definitely made yoghurt with frozen cows milk before, but it hadn't separated so different situation. It worked fine though, so the freezing process for cows milk definitely doesn't do anything detrimental to the milk.
As an aside, can you not re-homogenise the milk with a stick blender or something similar?