Without invoking any conspiracy theories, finding one body that was wearing an oxygen mask doesn't necessarily mean much. We know the wreckage was "messed with" in the days before any independent investigating personnel made it there. Finding a body with an oxygen mask on does not prove unequivocally that this person actually put it on himself shortly after the plane was hit.
It is actually much more surprising that so far just one passenger was found with an oxygen mask. If some of the challenger astronouts were still able to activate their emergency oxygen supply, why shouldn´t a certain percentage of passengers? After all they had almost 2 minutes time...
The lack of a substantial crater means that most of the fuel was burnt before impact.
Luckily all that is captured on video, so one thing we for sure know exactly is that the plane was not trailing a faint of smoke, and exploded upon impact in an impressive fireball. Crater or not, this is one of the rare real evidence we have so far.