What do you mean by this? If you mean players who are logged off, or who are on a different smp server, the command /r pay (username) (amount) will still work. If you mean sending someone actual real life dollars, mailing a check would probably be the best option.
Im assuming you mean paying a player out of game. Currently there is no way of paying someone with rupees outside of being in game. Correct me if I am wrong but I think there is a future plan to have rupees transferred within this site.