Just yesturday I finnaly get wiimod working fine. And I had the same problem. I would like to do wiisis FPS game with ability to use wiimod functionality in cut scenes or mini games.
For next step from Renevo developers I would like to see a flow graph wich can Enable and Disable wiisis controls.
For examaple, You playing your level as you did it in Wiisis, then goes a cut scene or mini game and in this time all controls are disabled, you can use just Wiimod Flowgraphs or Lua.
(One thing is that I haven't checked it yet, it might be already there)