How does a government "acquire" a not-for-profit entity? Such entities have no owners, so you can't purchase one. Did the government buy the assets, or what happened?
The other issue to consider is whether the nonprofit is now itself a governmental instrumentality. If the only member of the nonprofit is a governmental entity, there is a good chance that it is.
In any event, if the nonprofit has somehow failed to become a governmental instrumentality, and is still an ERISA plan and subject to coverage rules, I'm not sure how you could possibly apply them on a controlled group basis, given that such rules do not apply to governmental plans. You would, of course, still have to apply the universal availability rules.