Henry's supporters used this incident as a means to have him appointed as Colonel of the first Virginia Regiment and Commander-in-Chief of all Virginia forces. However, the Virginia convention, not trusting Henry's military ability, made him subordinate in all military matters to the Convention and the Committee of Safety. It was, in fact, a paper command for Henry was subjected to all kinds of civilian direction and interference. Subsequently, Virginia never saw fit to give Henry command of any forces that might see battle, passing him over for other officers. The final straw came when Henry was passed over for a Brigadier General's commission in February 1776 and he felt he had no choice but to resign.
Most of the senior Virginians, to include Washington, were very much aware of Henry's limitations as a military leader so it is not surprising that they gave him a commission without power or responsibility. Henry was a hero in Virginia; his fiery advocacy of liberty and his insistence on marching on Williamsburg to recover the gunpowder meant that politicians could not just openly refuse to give him a military command that most feared would result in disaster and the unnecessary death of soldiers. So, they chose this way.
I doubt that the Massachusetts Provincial Congress could or would have handled Dr Joseph Warren in this way. He was just too powerful.