I never really had a problem with her because I liked Allison as well, but I think after season 6, her character went through some of the same issues that Lana went through earlier, which was that they didn't know how to keep her around, but they still wanted to have her around, so they changed her drastically to the point where it seemed like she was more of a setback for Clark.
All that talk about him being a BDA was because Chloe had suddenly become smarter than him and basically commanded him around. He couldn't make any decisions without consulting her for a long time. Adding to that, they made her a meteor freak for a while, put her in the spotlight for much of the last few seasons, and had her marry Oliver while becoming Watchtower for the JL. Stuff like that made it more desirable that she would have died earlier in the series.