Unless its an annual leave ticket, I always use the ticket desk at the airport. Pick the right time if you can, and the guys there are pretty ok (even at 1am) - done it a few times and no problems.
Oh and if a paying pax is in the queue, allow them to be seen first - the guys behind the desk like this and will treat you with more respect when its your turn.
Back to staff travel - automate it like most airlines. But then what about Bahrainisation ......?