I'll probably wait until part 4 of the next chapter is finished until I read it.

I'd really like to read The Progressers before I make a judgment on how crazy or not crazy Kirito is regarding NPCs.
There is certainly something to say about treating the world you're in as the real world, though. The author is touching on what it is like to live in a fully digital world.

One of the best things about Fairy Dance was the dichotomy of how Kirito treated the game and how others treated the game. He treats everybody he meets as if he was meeting them for real and it really surprises people and has a strong effect on them. Just because you're seeing an avatar representing someone, does that mean it should be any different from meeting them for real? In the real world, you have people who act like total douchebags on the internet because of anonymity or that they feel like the relationships they would make don't really matter. You don't have to look far to find someone like that. I think it is something interesting to think about with the direction our world is moving towards regarding communication.

Kirito has had a pretty good reason so far to treat each of the worlds he has visited with super seriousness.
In SAO, his life and everyone else's was on the line.
In ALO, Asuna is in danger.
In GGO, there's a murderer on the loose.
In Underworld, he has no idea what's going on, so better to be on the safe side and be serious.

There are definitely some interesting questions brought up throughout the series about relationship and what being human really means. Is Alice a person? What about the other 'people" in that world? Is Yui worth treating like a human being when she's really just a collection of learned responses? Are humans collections of learned responses too?

I wouldn't really say the author is exploring these issues, but he is bringing them up and throwing them out there for people to think about while he tells a fun shounen story.

Asuna hasn't really been shown as being stupid either. She went to a private school and didn't really play games before SAO, right? She came up with lots of boss fight strategies and seemed to be a pretty good leader. None of her deductions really seemed unreasonable to me, given that she had talked with Kirito about some of this stuff and was very suspicious of Kikuoka.

Something tells me there's a LightCube with a backup of Kayaba. Seems like a plot point too good to pass up.