The plumber had no idea what he was doing. If the well is pumping undesirable water, the pump will pick it up no matter where it's located in the well. Now if your well is a low producer, you will have more problems than if he had left it where it was.
If you can't get any help from this shyster driller, check with your county or state. Whoever it is that regulates the well drillers. Then register a complaint. If this is a new house, call your builder. He should have to stand behind anything done in that new house for at least one year. If he is still using this guy, he would have far more leverage than you would over this guy.
The reason I'm not offering any advice is that the well was good for two months and now is showing nasty water. I have no idea what is wrong, but I am sure the driller does.