Unfortunately you are right. This scenario is not supported by our RadAjaxPanel because it is actually a wrapper around the MS UpdatePanel and injects the real update panel on-the-fly, thus modifying the Controls collection of the GenericWebPart which results in the error you get.
I hope that replacing our ajax panel with MS UpdatePanel in this case (which behaves in the same way) is applicable workaround for you. Please excuse us for not being able to provide more elegant solution for this particular situation.
the Telerik team