do not use generic RTV on it (if the silicone smells like vinegar then its oozing acetic acid which will cause more rust)
remove the strip and wash it with a brush, wash the area on the roof too, allow it to fully dry and then apply some rust converter on it, allow that to dry then brush some primer on it and reclip the molding back to the roof, you can use 3M double tape to stick the corners.
btw - how did you deduce that this is what lets rain water in?