1) Let's say the first missile strike was when the transponder stopped - at this point the plane had already started to deviate from its intended course - why didn't the pilots contact ATC to request clearance to land at the airport, or to request clearance to do anything? If the radio had failed at this point, then the pilots would have (should have) attempted to communicate the lack of radio through other means before deviating from the intended course, such as through the transponder.
2) If the first missile strike was the cause of the deviation, whether initiated by the pilots or due to the aerodynamic flaws of a strike, why was there a delay before the transponder knocked out? I still consider the lack of communications directly from the pilot to be troublesome since the plane doesn't seem to be too "out of control" and the descent appeared to be shallow.
Good chance that if the radio failed due to impact, explosion, fire or other major issue, the transponder also stopped working. Besides that, communication is never the first thing on the list when confronted with a failure. Flying the plane (keep it in the air) and navigating the plane (don't hit the mountain) are paramount.
If there was a sufficient issue, it would cause a stream of warnings, bells and lights in the cockpit, requiring immediate attention. If enough failures are present, you really need some time to proces it and again, communication is far from the first thing on your mind at that time. And setting the transponder, if it still worked, would be even lower on the list, both mentally and on the actual checklists.
regarding the deviation, is it already clear they did deviate and not follow the departure procedure, possibly cutting a corner (some flight management computers do that) or following a shortcut previously gotten from ATC?