Sad case...... really nothing can be done about the capacitor on the mobo, all you can do mow, is try to figure out how much of the GPU's heatsink you need to file off....
That will be the easiest way, remove the heatsink from the GPU, mark the area which comes in contact with the Capacitor on the mobo, use a Round file to cut thru the heatsink parallel to the surface (Of the backplate). and viola...... it'll fit like a glove, but you have to be very care ful while incerting and removing the card 'cos the sharp edge of the filed heatsink might damage that capacitor when you try to put it in or pull it out, be gentle and don't use excessive force....
it'll work fine.
Do all the metal work only after you have separated the heatsink from the GPU.....