You could easily include an alias file with your script for this purpose and then use alias myscriptsaliasfile.mrc ....
Given the issues I mentioned in my other post, I'd much rather see the alias command given the ability to create aliases in remote files then see what hacks and half-measures would be needed to solve the problems your suggestion raises.
Incidentally why are you allowing people to rename existing commands? Why not give them simple commands to begin with? After all, they have to know the name and purpose of each command in the first place to know what it is they're renaming.
