I think the reason for this "misnomer" is that consent when discussed as a concept has come to mean more than just "permission." It has taken on a broader mantle to describe the power over self-determination in human interaction, so that when someone says "my consent was violated," what they mean is that their power or right of self-determination (their ability to give consent or withhold it) was violated. This is how I use the phrase and discuss the concept, and I know many thought leaders do as well. We all understand that the act of consenting is the act of giving permission (i don't know anyone who doesn't know this), so I don't really think that's the problem.
As ideas evolve, it becomes necessary for language to evolve with it. :-)
RE: The Misnomer Files: “Violation of Consent”