Yeah, that is a totally unsupported use-case unfortunately. As I mentioned above the first release of the iPad player had very limited support for Maple Worksheets so we had to limit the app to only supporting the worksheets that were shipped with it. It took quite a bit of tuning to get even those working correctly. Adding your own worksheets has a very high probability of not working.
The iPad Player is definitely on our radar though, and it would pay to watch for updates to it in the (near?) future. The next version is targeted to have more complete support for all worksheet features and so would hopefully support your application.