Of course they do. Raiden is crotch-grabbed by the president (!) in Metal Gear Solid 2, he's raped by Volgin in Snake Eraser (it's supposed to be comical), Volgin also grabs and squeezes Snake's crotch in Metal Gear Solid 3, and there's prison rape implied in Mass Effect 2.
I find Mr. Bakhtanians' apology remarkable for its utter lack of any apology.