Your = God's or The Father's It is God's Will that will be done.

"You will be done" only makes sense if you are talking to a beefsteak. Here, "will" is not a modal verb but a noun. Your (God's) will. When speaking this prayer, the person means that God's wishes or desires (His will) should be done on earth. Because this is a direct address to God, we can't really substitute "your" with anything else. The "be" in the sentence has the simple present subjunctive meaning (a desired action), and nothing to do with future "will be".

this is the phrase Jesus said on the mountain; our father who art in heaven, ............thy kingdom come, thy will be done,on earth as it is in heaven thy will = your will, it means what ever you want (addressing God) you can do, either on earth or in heaven. the sentence is correct grammatically, (your will) should be your will not (you will) the word "will" here is a noun, I hope that helps