We have a very similar case in our mobile demos. What we did was a server-side detection, which determined if the request was ajax or not. If the request was ajax, we serve the page with an empty layout.
A thing to notice is that the problem you experience is due to the fact that each remote page re-instantiates a mobile application in its scripts. When the mobile application loads a remote view, it also parses any scripts and styles found in the body (if such is present).
the Telerik team
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