Not sure this would be a solution. In this case it seems like Protonmail wasn't logging IP but then was compelled to by law. So my assumption here is even if they stripped IPs, law enforcement could compel them to unstrip them going forward for an account. And that's what happened in this case.
That said, if there was a third entity that removed IPs for Protonmail, maybe that could get away with it. Kind of like how Tor is functioning.