Roni
Here is my opinion, I would use Meguiar's Scratch X 2.0 to remove the rust stain from your paint. I have used it in the past to remove scratches and paint swirls on small areas, it works well.
Just as an added test, I just went out to the garage and tried it on a rust stain I have been putting off removing. Well, no need to put it off any longer. The stain is gone and the paint is now bright and shiny.
Also, here is the phone number for Meguiar's Customer Care Center 800-347-5700. They could confirm my choice or may have a better solution.
Barry