Here's a new test version of KU with the new 'Exclude Formats' configuration option.
To use it, at the config screen, simply type in a comma separated list of formats that you do NOT want calibre to see as a 'supported' format.
Eg: Enter
epub to force Calibre to convert epub files to kepub during sending.
If for some strange reason you want kepub/epub files to be converted to mobi before sending, you could enter
epub,kepub
EDIT: Test release deleted.