I don't think what she said was that upsetting. From her perspective, Sam is the worst thing to ever happen to Dean. She had to have worked very hard to help Dean get to the point that we saw in 6x01. That sure as hell didn't happen overnight. Sure he was still grieving but he was better than when he first arrived on her doorstep. And then Sam shows up and Dean is instantly pulled into the drama and danger of hunting [Which to her Sam represents]. Dean's instantly filled with conflict; torn between his life with her and his devotion to his brother.

From Lisa's perspective, as much as she loves Dean and wants to be an island of love and normalcy for him, his last visit was a wakeup call. Dean can't heal, he cannot be the man he was during the year he lived with her- while he's with Sam. His issues will only grow and since Lisa doesn't know that Dean was turned into a vampire, she thinks the reason he lashed out at Ben was because of those issues. So in order to shield her son, she can't allow Dean back in her life. :(

But I'm still hoping that something will force them back together [and that Sam will explain what happened to Dean and apologize for endangering the man she loves and making him think he was about to die!].

Basically, she just told the truth. I suspected long ago that she felt something like that. I still think they'd be good for each other. Actually, I think Dean's the one with the stick up his ass. *ducks for cover*

i've never really liked Dean/lisa..
and i think what she said even if she think is the truth was SO STUPID... i may liked her a bit when she toled Dean to go with sammy...but then now..NOPE I DON'T !

While I do agree with what @fanfly said, I think at the same time what she said really shows a lack of understanding for who Dean truly is. Sam and Dean's love and devotion to him make up such an extremely large part of who he has been since he was 4 years old that they are pretty much indistinguishable from everything and anything else that Dean is. Sam is the one person Dean would do absolutely anything in the world to protect (ie. selling his soul), and Dean loves Sam more than anything; and that includes Lisa/Ben and the normal life they were beginning to share.

I understand how difficult it must have been for Lisa to welcome Sam back into Dean's life after, and I'll borrow from Cas here, "the broken shell of a man" who showed up on her doorstep a year ago was just really starting to have that normal-apple-pie kind of a life that she probably wanted with him since the first time they were together. I understand that Lisa loves Dean, that Ben loves Dean, and that she wants him to be safe and that she feels like when Sam is around Dean can neither be safe, nor normal. And I respect the crap out of her for trying to make it work with Dean after knowing that he would have to choose hunting at the end of the day, not necessarily because he wanted to leave them, but because in his mind leaving them (protecting them), and helping out Sammy was really the only choice.

I think in a lot of ways Lisa is jealous of the bond that Dean shares with Sam. A kind of bond that is so deeply ingrained that she can't even begin to fathom it. A bond that transcends everything, including death. And, I think, she just couldn't take being second fiddle anymore. OF COURSE, I think a large part of it had to do with Dean pushing Ben, like @fanfly said she didn't know he was a vampire at the time and actually trying to protect them by getting away as fast as he could, so she could only assume that the erratic behavior was caused by the return of Sam. Because Dean is different around Sam, he always has been, and I think a part of her is really frightened by hunter Dean. Because hunter-Dean is so different than 'taking Ben to baseball-Dean'.

Anyway, while I think I'm done ranting now, but my point was, I used to LOVE Dean/Lisa; she is absolutely without a doubt my favorite person that Dean has been with in the course of the show. And I adore Ben and Dean's relationship. I want Dean to have a somewhat normal life, but I want Dean to be a hunter too. I want him to have the best of both worlds. So really the reason what she said upset me was because I felt like Lisa was the ONE person who truly understood Dean outside of his circle of (Bobby, Cas, Sam) and then she said that and it led me to believe that there is so much about Dean and his motivations that she doesn't understand, so that upset me a bit. But, I am still rooting for them. Hopefully, someone will explain Dean and Sam's freakishly (amazingly) close bond to her so that she sees that they make each other STRONGER, MORE COMPLETE people, not the opposite. So for now it made me like them a little bit less, but I'm waiting (and hoping) for the writers to redeem her in my mind.

for me it all comes down to that dean had a family...something that he wanted for such a long time, dean has someone else in the world that cared for him and that he cared for back...thats why i love them together, and it breaks my heart to see dean loose another person...so yeah i want them to stay together.

Oh wow...fifthbitten took my comment right out of my mouth lol. I totally agree with fifthbitten on this one :).

the only way i could of really liked her - was if Ben would of been Deans son - that might sound really wong - but how sad were you when you found out he was'nt - after that i thought that was going to end of her - i think Dean only like ( the idea of her) - you know a wife , kid , house , - plus no hunting

Dean and Jo forever.