How can we change a Witness in an already executed gift deed

As you are the maker of the gift deed you have the option of cancelling the gift deed with the consent of the donee, which in your case is your mother.

And make a fresh gift deed. 

And to avoid future clashes with the witnesses, we would like to suggest you that it is better to register a gift deed as by the process of registering the gift deed the Sub Divisional Magistrate (SDM) becomes the witness of the deed.