Firtsly Layang resort and the airline (KK-LL) are pretty much reliant on each other there is only one way to get there and one thing (mainly) to do when you are there. As for being able to run a regular air service, this place is miles form anywhere its not boeings, they are small twin engined propeller aircraft. I would take there word for it, if the plane cant fly, then thats it, i thought there was something in the booking about this.
your booking was made through your travel agent in KL so presume they put the package togehter not LL. And they should be the ones responsible not LL, if not for booking the package but for not advising you corectly. I would suggest that buying a low cost (non refundable) ticket when going diving to this kind of place, is not always the best soluition. What if you couldn't get back in time???
At the end of the day we are talking about a US$900 dive package and a US$100 airticket, buy the better ticket in future and then dont worry about things like this, or insurance.
I found LL stafff very helpful, flexible and an excellent dive location.
As for no contingency plan, Sipadan isnt far from KK at all, or Lankayan, there are lots of options