Part of the original Mega Man's design document (shared in Japanese by Capcom themselves some time ago) has now been unofficially translated into English
Part of me feels like the health-as-timer mechanic was born from the developers approaching the game with arcade-style design in mind. That sort of thing works to make sure people don't play too long on the machine (a la Gauntlet or Wonder Boy), and while other games still retained it I don't think it fits well with the kind of game Mega Man turned out to be. (That said, I think the final product's completely useless scoring feature is definitely a holdover from this same line of thought.)