1) The betrothed woman is considered to have been a willing participant in the sexual relations if she did not cry out for help. This assumes there would have been someone around to be able to help her, which is why it differentiates between "in the city" as opposed to "away from the country."
So, whether it speaks of rape or not depends on whether she cried out in the city, if she was in the country, it is assumed to be rape and she DID cry out, but nobody would be there to save her anyway, so SHE is relieved of any guilt.
2) That is NOT rape, nor any other kind of sexual relations. It is saying that the young girl must be VERY young indeed to still be a virgin while living in the lands of the pagans. The girl was so young that she probably was not well versed in the paganism of her family and so could be spared. The boys were killed because when they grew older, they would turn on the Israelites and attack them for killing their families. The parents were guilty of their sins, and so had to be killed for their sins.
So, no, it isn't speaking of rape.
It should be pointed out that the death penalty was RARELY passed down. In fact, a Sanhedrin that condemned ONE person to death in a 70 year period was considered bloodthirsty. Yes, the death penalty was on the books, but that doesn't mean it was used with abandon, as some folks seem to think.