It's a very good idea.
I remember a lot of good ideas on the GMTK jam with the "Out of Control" theme, but here the change of control feels really good. Changing one movement button with a demonstration beforehand of what will be replaced is a good approach, reasonably player friendly.
The only time I got lucky was when the W button changed to itself on the move up :D You can also exclude the current assigned one from the set of keys to replace, so it doesn't feel like it's staying the same.
I really like the animations and style. "You can feel like an amoeba in this game". Very cool :D