This has always been the case with capital moves. It's meant as a penalty just for doing such a monumental task, not as a replacement for the rule.
However, the rule has never been "don't move your capital in time of war." The rule is "don't move your capital purely or primarily so that you can recruit closer to the front line."
Any realm that has lost its capital certainly has to move it to a new region. I can come up with some hypothetical examples where it could still be an illegal capital move (for instance, they have 2 cities left in the realm, one in the middle of their realm, the other near the front line, and they move it to the less central one for the recruitment benefit); however, in general, I think that realms whose capital has been lost should get at least a little extra leeway in these things.
Even that hypothetical is a very weak argument for punishment. There's a huge difference between making a decision to move the capital while you still control the city, and choosing the best of two options when you're forced to after the capital leaves in a hostile manner. Shouldn't be penalized when making a smart decision out of a bad situation.
