I do not know if it would work or not, but maybe but the sprites you do not want affected on a separate CanvasLayer node?
There is this Youtube video, though I do not know how helpful it will be:
Someone in the video's comments mentioned that setting the light mode to unshaded made it where the Sprite is not affected by the canvas modulate, which might be worth looking into.
Outside of that, I'm not really sure. I'll keep an eye out for other potential solutions.