If the company policy permits it and you want to, go for it. But I'd never try it without first discussing the precise details with the people involved in approving the expense. I have heard of companies that will split/share the savings of folks ticketing in Y rather than C/J when permitted so it happens a fair amount, but I wouldn't buy a Y ticket, upgrade with my miles and bill for the C/J that I didn't take unless the company explicitly permits it. Otherwise you're committing fraud.

It is also worth noting that such a scheme may run afoul of the IRS if you are a US citizen and are not declaring the "bonus" money that you receive. A group of NBA officials got in a lot of trouble for such a scheme at one point a few years back.