Okay, I got something working. I wasnt aiming at a scripting method either...

Left side of the tree is the original unedited version. I did mess with the priorities of the shadow layer. See how the top half of the cactus is lit up? Thats the tile I couldnt set a higher priority on. Had I just cut the shadow out as suggested, the line would still be there, just with a different shape. The half of the tree on the right has a full shadow layer on top of it. As you can see, it fully covers the cactus and puts it in shadow.

In the above image, the tree on the left is the original, and the tree on the right is the color adjusted one. It looks much brighter than it should, but when covered with the shadow tile below it, matches very closely. Not perfect, but close enough for govt work. It just always irked me to see a characters head pop out of the shadow under that tree when I had expected it to be in and stay in shadow. So shadow gets a higher priority so it stacks on top of other tiles under it. It does use an extra layer for the shadow, but I'll live with that.
Edit: If anyone wants to use that image, feel free, but it needs some editing. First off, the width of the image is twice the size of what you need, so crop the right half, and the shadow needs a bit of repositioning, but other than that, the colors are so close that they wont give you any difficulty.