Of course she can charge him for paying by check, in the sense she can offer him a smaller amount by check outside of the 403(b) in exchange for him agreeing to have the court void the QDRO. This may be the best alternative for both parties. The check she writes him would be considered part of the property settlement (and thus not taxable to him), so he could end up with as much money after taxes even if the check is less. Meanwhile, by writing a check, she increases the amount she will ultimately get from the 403(b) by more than the amount of the check (because he will no longer get anything from the 403(b)), without it being treated as a contribution to the 403(b) subject to the usual maximum limits.
Yes, they should have thought of all this before entering into the QDRO. But if both parties are willing to amend the QDRO, better late than never (unless the costs associated with amending the QDRO are so high as to make the whole thing uneconomic).