I'm not sure I'd argue with your crew. There seems to be continuing unrest, though a quick search gave me a 2009 report, nothing later (but I was just skimming). Surge in Mindanao kidnappings
Fishing boats were the biggest victims in the past, things don't seem to have improved. Island nations can have a lot of problems with communication and resentment between islands, let alone cultures. It seems that the southern muslim islands are the poor relations to the rest of the Philippines, and your Christian crew possibly considers them a serious threat to them. I don't think that reason will prevail, unfortunately.
We were in Sarawak in 2001, and the kidnappings in Sarawak caused a lot of dismay and unhappiness.