I would call the vet and explain to him/her the situation and perhaps have the assistant spoken to.  If you really like your vet then continue to go but, anytime that person trys to handle your little boy just tell her "no" that you would like someone else to help.  If she asks you why, just tell her you treated my little boy badly and you didn't appreciate it.  If she doesn't appologize then I would definately choose another vet.  Remember are pets can't speak for themselves we have to speak for them.  Let us know what happens.  We are all 100% behind what ever you do.