I agree with what Falk said about Malaysian Muslims. He said it better than I could, I would find it highly surprising that Malaysian Muslims would be behind this, because you are unlikely to find any sort of radical Muslim behaviour. The majority are conservative and go about their daily lives peacefully. It's always been a safe country like Australia or Japan. The political situation is different though, its basically a one party system, though its been challenged in recent times by the rise of the opposition. There have been peaceful protests in Kuala Lumpur about having 'clean' (bersih) political election campaigns. Its been speculated in the past that the sitting government have used dirty tactics to win the election, such as allegedly buying votes with increased immigration into the country... i.e. approve X number of Bangladesh/Indonesian/Fillipino immigrants, pay them money for their vote etc. The opposition have been livid about that. Just last week, the opposition leader Anwar was supposed to contest the by-election at Kajang but he was sentenced to five years prison for sodomy (which many people thought the charges were dubious at best and you can google it up) and a dirty tactic the government used to win the election. If the pilot is a fanatical opposition supporter, then I can see the link, but even still its far fetched that he would pull off something like this on his fellow Malaysians.
Speaking of which, like others, normally I don't see an issue with the pilot have a pilot simulator at home. BUT it would coincide with how well planned the whole thing was and how flawlessly executed it was.