An idea to add tile paint features on a non-tile based editor like C2 is something like:
1.
<img src="http://dl.dropbox.com/u/2472278/Images/1.PNG" border="0" />
2. Scene Editor
<img src="http://dl.dropbox.com/u/2472278/Images/2.PNG" border="0" />
3. When double click
<img src="http://dl.dropbox.com/u/2472278/Images/3.PNG" border="0" />
You get the idea. The brush icon is to emphasize that you paint the tiles. In the painting window of course there must be a tile pallete to pick the tiles just like tiled editor and similar.
There's several ways to implement that of course , and i believe it's compatible with current C2 workflow. One point that would have to be addressed with this system is collision. Maybe a grid based collision body.