OK, I see the pictures now. They are small but it helps.
I'd wire brush the area then paint with POR15. You don't have to remove every speck of rust - just get any loose flakes of rust off.
There is supposed to be a drain hose at that location - both sides. They can get clogged and thus allow water to pool and even over-flow to get the floors wet. I use a small diameter plastic hose (~ 3/16" OD) to fish out the inside of the hose and make sure it drains freely.
I thought I would post some photos of the rain gutters so you can see what they should look like without rust. The photo of your drivers side looks like there is a lot of build up of some kind just behind where the top bolts to the pillar. Something does not seem quite right to me, there is a lot of something there and you may want to investigate further.
This is the photo of the drivers side rain catcher. The area is basically a rain gutter with a hose connected to the outlet at the low point. You can test the drain by pouring a little water into it and make sure it comes out the bottom near the end of the rocker panel just behind the fender. It should run through very quickly unless the hose is plugged or ripped.
Photo of the passenger side from a different angle. This will give you a perspective on how the gutters catch the water and drain it out of the body. There are two collection points on the back gutter that should have hoses connected to them. They route down to the side and out the bottom near the side gutter hoses. On this photo you can see the new clear plastic drain tube from the back drain and the new black drain tube from the side drain. You can also see the hole just above the gutter where the top frame mounts to the body.
I hope the photos help you visualize how the system works. You will need to expose the gutter area to deal with the rust properly. This will require that you remove some of the interior black trim along the gutter. You may also have to remove the top in order to get at the rust and clean it out. That is not a difficult job, just a bit time consuming. It helps to have the seats out to get access to the back.
Let us know how it works out. Photos are always welcome.