I have no Idea how much damage was done, but something went wrong. My sujestion is if someone want’s to tinker on my transmission fluid after it drove in to the garage fine they are responsable for the repair. My guess would be that you havent touched your fluid in quite a while so when they said it was over full then you should have been weary, fluid does not duplicate it self. If they would have said it to be low then definitly put some in it.
As far as damage is concerned you should consult with them, how long did you plan to keep the Eagle ? Sometimes transmissions that make noise still hold out for quite a while. It sounds like a band is wearing inside the transmission, you should have them pay to have the filter and fluid changed and see if this makes a diffrence, also had Lucas transmission oil with the fluid to help it along.