No, there aren't really better options, we are stuck with workarounds until it is addressed. This concern was raised very early on by beta testers. It is a known issue they want to resolve and are working on resolving, it just isn't resolved yet. I can't say what the odds are of having it addressed by final release, but I am not holding my breath.
Not to nitpick on semantics, but they are important in this case. A user can run more than one instance of ArcGIS Pro, just not on the same machine at the same time. The current per-user licensing model allows a user to run ArcGIS Pro on up to three machines, unless offline licensing is enabled, and then the limit is one.
