To be clear I'm not as familiar with this for non-profits.

But generally yes, if much of your compensation is bonus based most executive contracts will have a mechanism for pro-rating or just paying out future bonuses.

This sounds a bit like it was something of a mutual parting of the ways so sometimes boards will payout other bonuses like Retention Bonuses (A bonus for staying at a position, frequently with another job offer at hand) even though the person is leaving. It could also just be a bonus triggered by the board choosing to part ways with her that was part of her executive contract. Proving a firing is "for cause" is frequently difficult so sometimes if there's a desire to replace a senior executive it's easier to just pay them off.