Clicking a pixel again (same color) would delete it, in lieu of an eraser tool. That would shift the burden of clicking twice to get your desired result to when you were deleting a pixel of different color.
OTOH – an eraser tool is really just a toggle button, isn't it?
But since there's no color palette or eyedropper, finding the same exact color is virtually impossible… so right now the way that you describe wouldn't really work.
And the eraser tool would be easy to implement technically, but I'm just not sure yet it's the best solution, or where to put it.
I'll probably end up doing something like holding shift while clicking will erase the pixel.
OTOH – an eraser tool is really just a toggle button, isn't it?