Ahem, maybe not.
I don't think there's a lot we can do. They can be valuable tags to keep around but there's currently no feature which allows us to make sure somebody posts another tag. The best we can do is improve the short wiki text so that the description they see in the tag suggestion box tells them they shouldn't be using it on its own.
It might be worth submitting a feature request on MSO (they tend to get more notice there) asking that we be allowed such "special" tags. Tags that don't count toward the tag total so that the user must use another one. I don't know how best to phrase that or I'd submit the request myself.
But in the short-to-medium term we just need to correct people...
Somewhat later I started a little petition to get version tagging brought up to a usable state. Like it or not, version tags serve a purpose to more than just this site, it's just a shame there aren't controls to stop them being abused.