for your first . if the storm night was rape it was poorly portrayed since that was not the impression I got. since Inoda had been using the sad puppy act the impression I got is that he probably begged until he got away with it as shown by the images. first a hand job then he progressively moved towards sex. remember she lied to kirito when he made the phone call. it was not rape it was "yoga". again this also adds another point to the list of contrived reasons for that sex scene.As for the real world sex happening before virtual sex, there is a real world and game world reason. The real world reason was Fujino decided to split the game into parts and my guess is he wanted to end the game with a bang (literally). The game world reason was Kirito suddenly asked Asuna to leave with him soon so Asuna decided to end things with Inoda. Then Inoda was forced to keep Asuna by raping her into submission. If this was another NTR title then Asuna would have fallen during Lustful Night. But Fujino made her resist and now in Part 2 we are getting back where they were before.
So you expect Asuna after being raped in Real Life to want to have Virtual sex with Inoda soon after? It took her until now in Part 2 to finally forgive him and you think she would want to a physical relationship with him in VR because what, she is horny?
Inoda picks the key for no reason at all.
a storm happens
kirito's phone is not charged
he goes to sleep.
As for your second question yes I do believe it. remember porn logic is not real logic. if she was raped I doubt she would even feel comfortable to have sex with anyone she barely knew (like Inoda). it is a good thing inoda is portrayed as non threatening since SAO's rapist seem to be the forceful kind. but again if we use anime logic for this porn game the story would not even happen in the first place.