The idea that the Clintons killed the low level party network with their DLC/Third way politics is a view strongly held in some cirlces. And I think it is correct up to a point. But it was certainly not the only thing working against the democratic party and the party organization.
As for a Hillary Clinton nomination, I wouldn't support it. And the Republican's would have to come up with a pretty bad canidate before Hillary would win the "Who would do less damage to the country?" decision.
I think she will have a very hard slog to get the nomination. Exactly because there is a significant chunk of the low level party organization that doesn't like her, and those votes are very important in getting the nomination.
She would also face a hard election if she was the nominee, though for somewhat different reasons. I think there are a lot of middle of the road people who will remember Hillary as being the less likeable half of the Clintons.
I would be very surprised if she didn't try though. 2008 is really her only chance, by 2016 she would be too old.
Jay