If the experience at AA is any indicator, this will result in semi-chaos that will, of course, be blamed upon the remaining agent for "not being efficient and able to multi-task."
Once boarding begins, the agent is the only means of communication between the flight crew and catering, the ramp, etc. The flight attendants can not leave the a/c if there is even one passenger on board. In theory if there is a catering issue for instance, the cockpit can call the tower who can then call catering. However, IF the message gets passed on--doubtful during high traffic ops--it usually is so garbled that the wrong catering is brought to the a/c, if brought at all.
When there are seat dupes, the passengers are going to LOVE having to go all the way back up the jetbridge to the podium to get the situation corrected. Whose going to let the gate agent know that the overhead bins are full and they need to start gate checking carryons?
Of course, the agent could just shut down the boarding process periodically, run down the jetbridge to check for problems, then run back up. Yeah, that's the ticket. That's sure to work. As I said at the beginning, all this would be moot if the agent were just more efficient. <_<
I realized within 2 months of starting flying that the gate agent has just about the hardest job at the airline. Nothing in the past 4 years has changed that opinion. Good luck to you guys.