I've just started working on a project which a) uses .NET and a fair bit of AJAX, and b) must comply to AA accessibility standards.
Are there any approaches that can make use of the positive aspects of the toolkit, while minimising the negative effect of the poor html?
You'll need to check ASP.NET MVC, which is a new approach in ASP.NET arena to create web applications.
That's controlling what's going to render and less auto-generated code, so I believe this is your way to go, isn't it?
While I see what you are getting at with the semantics of ol/ul vs div, the use of a div does not constitute "poor html". It's fairly proper to use the div for any block (styled or otherwise) inside of a HTML page.
To get to your question, about the only thing I can think of is for you to make your own controls and control the HTML rendering of the control OR you might be able to make custom versions of the controls in the kit (ex: accordion) and then override the rendering of the control. This would be a lot of work and really in my view unnecessary.
WCAG 2.0 Quick Reference