Easiest thing to do is to install to a new location. That will avoid the checks completely. A hacked thing to do is to fake the File.Version
column in the MSI but that will only get you through this once, eventually you'll need to get to a new location to address the problem.
You could also set the REINSTALLMODE
to include "a" but that will just create all sorts of grief for you lately, so I can't really recommend that as an option.
Note: The AjaxControlToolkit guys did give you a huge headache. If they renamed their .dll, that would be the most helpful. Seems like the least they could do since they just broke their world so badly.