It's not an issue of putting jQuery into noconflict mode; noconflict mode is installed. The problem is that those plugins ignore the fact that jQuery is already installed and they add a second copy. The second copy tries to override the first, and things stop working.
You can try the solution someone else found here:http://www.shape5.com/component/option,com_smf/Itemid,75/topic,31665.msg127436/#msg127436
Let me know if it works, and I'll see if there's a way to implement something like it into the framework.