Hi Pfuller,
I grew up in Sabah and now living in the USA, it's sad to see the situation in Sipadan area, I feel your concern. Here is what I can tell you as someone connected back home and in Sabah.
First if you still have desire to dive in Sipadan, which I think most divers shouldn't miss if they can afford it, there could be a safer way. What I heard from people at home is the kidnapping happen during the night, those terrorist could come out from the water and attack tourist who sleep and stay at the above water hut/bungalow. Since it's night, tourists get caugh off guard and do not have chance to run as you only have a narrow "bridge" to run to the main office for help.
When I first visit Sipadan, I stayed at the Seaventure resort (you can see my journal here: http://www.mosesong.com/travel/sipadan_trip08a.htm). It's an oil rig that get converted into a budget dive resort. To get up to the oil rig, you need to get on a lift that climb 2 story tall. It could be a safer place for tourist as terrorist will have to climb that high to get to the resort. If you look at the structure/column of the oil rig, it's not easy to climb unless they do it the James Bone way, he he. You can contact Seaventure people and ask them about safety feature like 24/7 staff patrol the perimeter, structure of the oil rig etc.
By staying at Seaventure, you could be safe at night, and during the day you can go on your diving business as terrorist don't come out during the day and there is coast guard on Sipadan island. Seaventure is just right across from Mabul island.
If you don't want to go to Sipdan, Layang Layang is the place to go. Like Drew say, it's popular, but there is a reason. In the book "50 places to dive before you die", the author explain why Layang Layang is popular. And for South East Asia area, that's the place to see school of hammer head shark, but they could be deep and the season is from March to May, but not sure what's after May. The resort close from August until December due to monsoon season.
East coast of Sabah have some small unexploid area do dive, such as "Pulau Tiga", and another area that I forgot the name but I will go there next year, In term of land activity, Sabah has quite a few things to offer. In you go to Sabah, you shouldn't miss "Mt. Kinabalu", which is in "Kundasang" area. Mt. Kinabalu is the tallest mountain in South East Asia and second to Mt. Fuji. You can spend two days there for the Mountain trekking, or just stay at the village at the foot of the mountain to enjoy the view and the nice climate.
I hope this give you some idea about what to do in Sabah.
Moses
As far