I can imagine there are a bunch of different solutions to this one. I'm normally not that concerned about using too many tools, but this one required more interface tools than non-interface. It'll be interesting to see how many different ways people lay out their interface tools!
Instead of adding the error I went the the preventative control: Let the user select the calculated variable and let them know the amount in the selected variable input will be ignored for the calculation. The Error Message tool is useful, but I would rather make the workflow error proof instead.