The bad news is that trains running through southern Thailand have already been targeted a few times; the good news, in a rather limited sense of the word, that it's been soldiers and one unlucky Thai conductor who got bullets in their heads. Also, if it's any consolation, the international expresses to Malaysia have (AFAIK) not been targeted and run along the shortest possible route (Hat Yai-Butterworth) through the area in question, problems have so far only occurred on the trains the long way down and across (Hat Yai-Sungei Kolok/Tumpat, which passes through every one of the 4 Muslim-majority provinces).

I wouldn't worry about it too much -- if it's any consolation, statistically you're far more likely to killed by an insane tuk-tuk driver in Bangkok or a motodop hopped up on yaba in Phnom Penh.

If you still want to fly, you can connect from KUL to all sorts of places. Eg. take the train from BKK to Surat Thani, hop over to Phuket or Koh Samui, fly from there to KUL and straight back out to Penang/Langkawi. Then hop on the train again and ride back to KL and onward to Singapore. All flights (except anything involving Koh Samui) cost peanuts on Air Asia.