I'll play devil's advocate a bit to figure out what you're getting at:
if the government were to forbid everyone from running any non-free software whatsoever, would that be a bad thing, a software freedom issue?
would the rationale that the goal is to stop people from being victims of malware not be a good one?
one could argue, as we often have in public tenders that demanded software freedom, that no software has the restrictions that render it non-free built into it; any piece of software could be made available in a freedom-respecting, thus no software is really excluded, it's only the abuse that comes with it when it's non-free that would be excluded
That's a very interesting & useful devil's-advocate argument.
I think your own answer is the most sensible one: the freedom doesn't come from the bits intrinsically, it comes from rights (and information) alongside the bits. Computers runs bits, but humans edit source code. Thus, a law saying "users can't run non-free software" wouldn't make sense anyway -- the way to legislate that would be to require that suppliers can't *supply* non-free software. E.g., just as HIPAA law (in the U.S.) requires that your doctor give you the primary sources of your medical data when requested, including X-ray images and everything, a software freedom law would require software suppliers to supply source code. The user wouldn't be the subject of the law, the supplier would.