Sounds like you might have wanted to read up on issues with the motherboard that you have. This is an all-too-often occurance with home-built machines. Unfortunately, motherboard manufacturers don't always follow all the rules on capacitor placement. The best way to avoid this problem is to do research on the board and heatsink combination that you want to use to ensure that no one has had issues like the one you speak of.
If you took the capacitor off, your motherboard wouldn't work.
Is it the heatsink clip that is interfering? If so, I have seen some people do some fancy bending of the clip in order to "fix" the problem. This creates other problems though. It would be safer to buy a compatible heatsink rather than resort to modifying the heatsink.