They weren't naughty, it's a normal route that plenty of airlines fly. Flying over conflict zones is completely normal, I've flown over Afghanistan heaps of times and even over Iraq the year the US invaded.http://www.washingtonpost.com/blogs/wonkblog/wp/2014/07/17/a-real-time-picture-of-how-flights-are-now-avoiding-ukrainian-airspace/
This link shows commercial flights avoiding the area - one that is the cheapest (fuel wise) to fly from western Europe to SEA. MH was a little naughty, flying over a war zone to save on fuel.
No one knows who did it or why, mistake or not, everything is speculation.