I'm glad I'm not in the position of having to decide a policy like that. Seems like either way you decide, there could be horrible consequences, and you'll second guess your decision.
Remember that you don't decide to give the guy a carry permit, the state does. If they believe he is worthy of being trusted with carrying a firearm, then perhaps that should be good enough. But the idea of requiring additional training, beyond what the state requires, makes sense in both a legal and moral way -- you are asking the employee to take the training that is useful for that particular tool (just as he would receive training to use a forklift before he could drive one) and if you were ever sued, you could point out that a) it was the state's decision to issue the permit, b) and you went beyond their requirements in your workplace policy. You might even hire a firearms instructor to create a class that deals *specifically* with the situations that might be encountered in your workplace, and trains on the exact responses you want in those situations.
Good luck.
Woodstock Doug