I didn't know anything about this, never heard of the show, but I love your analysis.
Hear, hear as they say in England! :)
I had to go and comment on the article you linked to and set them straight!
Plus, surely, if they don't like it - isn't that what fan fic is for? Get a grip, people. Much as I hated Josh with Amy I kind of loved it too. (the second time round - once I knew it was all going to be okay in the end...!!)
There are normal fans, and then there are the crazy ones ... it doesn't matter what they're fans OF, but they obsess so much they ruin it for others. Or, you know, something like that.
You're so lucky, getting to watch Chuck for the first time. I'm jealous (grin).