Incase you were wondering what this part of your car is called, it's called the window sash. As these cars get older I'm sure I won't be the only person with rusting sashes although I've never seen a car with rust on the sash as bad as mine.
I had planned on painting these because I figured they were part of the door and would be next to impossible and expensive to replace. It turns out they are very cheap even by Canadian part prices. I only paid $30 for each side.
The parts you will need are:
72731-SNA-A01 SASH, R. RR. DOOR QUARTER
72771-SNA-A01 SASH, L. RR. DOOR QUARTER
If you're not replacing both sides pay attention to what part you order and don't be alarmed when you receive the part, they are about twice as long as they look because only half of it is exposed the other half is inside the door.
I haven't done this repair yet, I planned to do it today but it snowed so I'm stuck inside so I'll tell you my plan of attack.
You have to remove the door panel, there are plenty of threads on this, it shouldn't be too hard.
This is a tinting video on a Honda Accord, they remove the rear quarter glass and it seems to have the same setup as the Civic.
I hope this goes as smoothly as I think it will tomorrow!