Hi,
you can try negotiating with them on the number of dives, play with the total numbers, you can opt to takeover her day dives? Or, go for what maybe more practical for yourself.
Or, go for it and forget about the money. Afterall, you are there to enjoy. Or, try SMART any other resorts that can offer you the flexibility.
What can be worse?
Hey, just thought of another place, check mataking out, they are having some promo not sure if it is still valid. Mail their resort marketting director think her name is Linda. Maybe she can help you. They do Sipadan as well but more limited to number of diving due to the distance. Am sure your GF will love that SPA. I have personally not tried mataking but through reviews, not bad and hey not bad.
If you stay on the mainland, you can definitely make some cost savings out of your day dives. But remember, no night dives at Mabul or the Rig or Kapalai cos usualy they do not do it. As for resort, mainland hotel is not bad but the beach is a definite no no for your girlfriend. Hope you can resolve this.. and really enjoy the trip.
Happy Diving !