"The mystery of life isn't a problem to solve, but a reality to experience"
I agree with David. We always played it by using the card you removed from the Ottoman's hand.
The card text (First edition, may have changed):
If Knights of St. John are on map, not under siege, and connected by 1 sea zone to an Ottoman-controlled port, draw 1 card at random from Ottoman and contribute CP value to St. Peter's construction. OR If Knights are off-map, Hapsburg adds them to a Hapsburg-controlled home port; the port space then switches to independent political control and a fortress is added to the space (if not already fortified).
It seems pretty clear to me, there is no indication you use the Knight card's CP value.