Hey! Was planning for a similar trip to Cebu few years back and I had the same concern with you - should we swim with the whale sharks or not? My husband and I decided against the idea (and also we were running out of time) after reading about the state of whale sharks in Bohol, Cebu.
I saw a recommendation from someone to swim with turtles on a neighbouring island though: https://www.dontforgettomove.com/swim-with-turtles-apo-island/
Perhaps that's something you can consider? All the best for your trip!