I know there is a glitch with the sapling where the old tree doesn't go away.

Is there anyway to avoid or fix this glitch on console, because I would defiantly like to finish it this way.

I didn't even know the old tree was supposed to go away. I just thought it was supposed to look stupid.

Nope, no way to fix it on console. I always finish the quest the other way because of this, I prefer to see the tree fully bloomed than dead and barren.