Actually comparable to rape rape? No, I don't think so. But it's definitely a violation. It'd be like reading someone's diary, wiretapping them, or taking secret pictures of them in the shower. Depending on the intent of the mind-reader and what was done with the information (is it made public, for instance) it could be absolutely devastating. The psychological effects of having a sensitive or embarrassing secret exposed can be very bad.
These particular examples are both somewhat justified because they amount more to searches by law enforcement... albeit probably warrant-less ones. I'm assuming SHIELD is allowed to do stuff like that, although they really shouldn't be (IMPO). The Spider-Man scene is particularly disturbing to the reader because a) we know what his secrets are and why he tries so hard to keep them secret (to protect his family), and b) we sympathize with him and know that unlike Crossbones, he's not a psycho criminal.
So. Rape? No. Strip-searching, warrantless wiretapping, creepy secret photography, "enhanced interrogation," interrogation without access to legal representation, revocation of the right not to incriminate oneself, and a dozen other reasons to be illegal and immoral? Definitely.