No, the Pentagon did not murder Michael Hastings, because he likely died of a substance abuse issue that led to his death. The Pentagon would have its work cut out for them if they tried to silence every journalist that expressed an unfavorable opinion. Yes, Michael Hasting's death was unfortunate, but it cannot be said to have been at the hands of the Pentagon.
It is clear that Michael Hastings was murdered, but I do not believe that we can know for sure that he was murdered by Pentagon officials. It is quite odd that Hastings' vehicle was on fire. There is video footage showing that Hastings' car was not followed when he crashed.