my mk 5 gti had this problem, i took it to vw got told it was the paintwork warranty that would have covered it, not the corrosion warranty so i got it repaired myself. A year and a half later i met the new owner of the car and was telling him what i had done to the car and the rust is back already, I think best bet would be repair the damage and get a bit of clear vinyl put over the area
I've just had a look on ELSAWIN and this problem is documented on there, the official fix is as follows:
Customer statement / workshop findingsScratches (see illustration 1, red arrows) in the inner side panel on the C pillar - only vehicles with 4 doors.
Illustration 1
Technical backgroundDirt particles in the sealing lip of the window guide rub on the paint of the C pillar when opening and closing the door.
This complaint may recur after the chassis break(10.2004) - caused by very unfavourable or incorrect adjustment of the door.
Production changeBetter contact of the window guide to the side panel. 
From Chassis No.: 1K5W127000 
 1K5B068000  
 1K5P042000 
 1K5D009000 
Measure• Perform the following procedure on the left and right side: 
• Remove scratches:  
• Polish or paint, depending on the degree of the damage. 
• If painting is necessary, only spot-paint the affected area. 
• 
Protect the areas by sticking PU foil part number: 1K4 809 387 on the contact area of the window guides. Part number 1K4 809 387 includes the foil for the left and right side.