There are many reasons that Barker could have said that he "vaguely remembers" her and is lying - he doesn't want to become a big ol' suspect (with the appropriate news coverage that could endanger his position and community standing), he doesn't want his private life in the newspapers, he DID help her run and doesn't want to help track her down, etc. You can see what happens when a guy admits having an extramarital affair by opening up the newspapers, imagine what it would have been like in 1974.
If she went to start a new life, it was easy to get a new SS number and identity back then, especially at her age.
Has anyone seriously looked into her ex? She spoke to him on the night she was supposed to go to Colorado; it doesn't sound like there is any confirmation that she ever left for Colorado, and her ex definitely had motive. He was one of the last people to see her alive.
For that matter, Barker's wife had strong motive. She would have seen Vickie has a "homewrecker" and responsible for their marital problems. Heck, Barker's wife left him in Colorado even though he had pneumonia! Maybe there was a reason for that.
Both were in Massachusetts at the time of Vickie's disappearance, her last sighting. Both would have seen her as "ruining" their marriages. Both, IMHO, had strong motive for murdering her.
I don't see Barker as having a strong motive for killing her, he and his wife were already on the verge of divorcing (they separated the following year, and his wife left him ill in Colorado, something I'd never do with my spouse, and I'd wager most of us would not leave behind a spouse with a serious illness.)
Typically, in cases like these - if the husband has no intention of leaving his wife, he may kill the girlfriend. If he does want to leave his wife, he may kill his wife. Barker fits into the latter category; I don't see any motivation for him wanting to kill Vickie.