I had a consulting gig once that was going to pay for a business-class USA-France round trip. I asked the client if it would be OK for me to buy an economy ticket, upgrade it with miles, and bill them for the J fare. They OK'd it, so I did. (As it happened, I only upgraded the return, since I knew the BOS-CDG flight would be nearly empty and I'd be able to get five across to lie down.)

That wasn't an employee reimbursement situation, but a similar approach might work there. I've read here of companies that let employees fly with miles, instead of having the company buy a ticket, and split what the travel would have cost. Not full reimbursement, but still a good value per mile if you're talking about international upgrades.