Hi CrashAlpha,
if you have access to Audiobus could you try this approach - essentially designed to allow you to apply 3rd party effects apps to a Cubasis track - but without using an effects app in the Audiobus effects slot?
http://www.musicappblog.com/diy-send-effects-cubasis/
It does at least mean that you get the new track straight into Cubasis without having to go to/from Mediabay - although you still have to clean up the original track, etc.
Good luck and best wishes,
John