I'm trying to send out invitations for a church member's two sons who are both graduating this month. She told me that they would like any monetary gifts to be given to the church instead. How do I word this on the invitations?

You could say "money in lieu of gifts would be appreciated". Then they could give whatever they were going to spend on a gift.

I think its more a case that they want a donation made in their name

"In lieu of a gift please consider giving a donation in the name of (the sons) to (the church name)"