Some people may be over-thinking this.
It doesn't matter what Harbaugh thought coming into the interview - OR what his agent was leaking to the media. and make no mistake, a lot of the buzz was generated by agents leaking to the media.
In the end, the two sides sat down, they talked, and both sides decided that this was not the right fit. Harbaugh sent out a tweet complementing KAM and the Vikings.
it's like a blind date. at the end of the night, you don't hate each other, but you decide the chemistry isn't right and you're not going to go out again.
I think it's as simple as the Vikes want to go in one direction, and Harbaugh wanted to go in a different direction as far as the QB, roster moves, etc.