You can do this.  The biggest problem is if your employee would want to accept an altcoin as payment, as usually all coins need to be converted into Fiat anyways in order to pay for most things, and the trading could involve some waiting, or loss in pay if a coin falls in price.  Also the problem with needing to pay taxes on the cash you pull out, assuming you will be paying proper taxes to begin with, would mean the employee would be double taxed if they were paid in Cryptocurrency.  It will work better in the future assuming a few cryptocurrencies take off, and could be used to pay almost everything.