Daenerys and Khal Drogo's wedding night is not the rape we witness in the show.

In the book "A Game of Thrones," though Daenerys didn't want to marry Drogo, it is explicitly explained that Drogo managed to seduce her. Most importantly, he blatantly asks permission to have sex, and she says yes (without lying — it's a point-of-view chapter so there's no speculation and her thoughts are described). In the show in season one, Drogo rapes her. We see her cry while her clothes are ripped off and, yeah, it's rape.

However, it's worth noting that Daenerys is 13 years old in "A Game of Thrones" and Khal Drogo is supposed to be in his late 20s. So even though she said yes, it would still be statutory rape because she's underage. In our world, at least. In Westeros, who knows what their statutory-rape laws are?