If it turned and were to follow established corridors, I can't imagine neighboring militaries would be particularly concerned. Even if they were paying attention to the transponders themselves, they might figure it was some sort of technical trouble--as long as the aircraft stays in the corridor, who cares? Some idiot flying along an established route without his transponder is a problem for ATC, not air defense, and that seems to be the best explanation for #1 and #3, probably even #2. Sure, Vietnam noticed and tried to inform Malaysia, but countries upstream from the route might not have cared (they probably wouldn't have seen it turn, either).
But you're right, Malaysia hasn't done a stellar job organizing the search and recovery (understatement of the year aware goes to...). The real problem, though, is that no one has any idea what's going on.
I admit. There's something fantastical to consider about a plane, under control of a rogue pilot (or pilots), clandestinely flying to a location for possible future use in an elaborate terror plot. The only caveat is that the logistics of such a thing would require so much preliminary planning in terms of fueling, storing/hiding the plane somewhere, or outright repainting it, that it very nearly requires the resources of a state actor or another determined (and secretive) foe. And who would be the target? The simplest solution, then, is to speculate that there was some sort of emergency on board, the pilots became confused (or incapacitated and the plane was operating on autopilot), and the aircraft is now at the bottom of the sea.
Returning to the article: It's easy to blame countries near the Indian Ocean of being highly secretive about their capabilities. I'm sure they are, of course, (and certainly need to be) but there's something about the elaborate hijacking plot that seems amazingly complicated and difficult to pull off. Moreover, as time wears on, the probability of being discovered increases, and I'm sure other states (Israel) might be keeping an eye on potential suspects (Iran) for such activity anyway, simply out of paranoia. Further, how easy is it to disappear a plane and keep it hidden for weeks, months, or indefinitely? One instance [1] comes to mind, but with 239 people on board...? That's to say nothing about finding a runway large enough to land such a beast that is also not well monitored.
I'll say this: It'd make great fiction, certainly, but I think the crux of the matter is something we don't do well as humans. We don't like to admit that we don't know the answer. And this could become the mystery of the century if it's never found. However, I'm inclined to believe it was an emergency of some sort (at least I hope). But, the only thing that doesn't mesh well with that theory is the engine monitoring data, but we might very well discover there was a valid reason for that (incapacitated pilots?).
For the sake of the families, I hope something is discovered soon--if only for closure. I can't even begin to imagine the pain they're feeling not knowing what became of their loved ones.
[1] http://en.wikipedia.org/wiki/N844AA