To state the obvious. You have a conflict in interest. This woman is interested in polyamory and your not. I read somewhere that many marriages have an unspoken rule that cheating is OK if it is not local and not spoken about.
net127 » The New Monogamy coins this as "Don’t ask, don’t tell."
You have to decide for yourself what is acceptable and what's not. Maybe she is so wonderful that you would rather be with her and allow her to cheat than to leave her. But, I bet you're worthy of better. Cron and the Colonel are probably right too, she will see you as weak if you allow it... Unless maybe if you were cheating as well.
Personally I wouldn't want to play this game. To me, her doing this behind your back is not acceptable. I believe communication is the key to a good relationship. If she asked you first if it was OK to have a relationship with your boss and you agreed, then well you agreed. She is either afraid to be honest with you or doesn't respect you enough to be honest.