Windshield weather strip leak and rust

Hello,
I know it's a long read, but I'm desperate here!
I desperately need help here. When I bought my 2012 Chevy Malibu, it had a problem in the windshield. The rubber weatherstrip was partially worn out and it leaked whenever I washed the car (*it doesn't rain during summer here) so I just taped whenever I took it for a wash. It started raining a couple of days ago and all hell broke loose, so I took it to the Auto-Glass guy. He removed the windshield, cleaned the edges, removed the rubber seal and sealed the the windshield back with black silicone sealant. Now Here is what is making me desperate. Two days forward, the seal job is not a success as it leaked today when I washed it today (very little ). The biggest problem is a a 4 inch RUST I just noticed exactly where the leak is. Apparently, it's caused by the rain. Tomorrow I'm taking it to the auto-glass shop again and I need advice. If I apply the silicone sealant on the outside, it will probably fix the leak, but does silicone help with stopping the rust from spreading?. I really need any advice here, I'm desperate and I wanna avoid any paint job or buying a new windshield. Thank you.