Well, you could just block out the button, right? Or, if worst comes to worst, just change the commandset of the building that builds the unit to include the unit when upgrade is purchased (I know this can be done; there must be a better way, however, but I haven't looked into it :P)
Take a look at the Pathfinder code, that's a similar idea, only using Generals Ability as opposed to Upgrade.
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