I don't use a drill. I've done a few 560 pivot mods and some with pivot barrel change outs and low rider pocket clips with thumb stud conversions now for forum members. With all the rebuilds of FRN Spydercos I do for members around here I've found that a thin kerf cut off disc by Keystone (non reinforced type) works best with a variable speed Foredom foot controlled dremmel to take the heads off those. I zero in on the smaller head size on most unless they are relatively the same on both sides of the pivot pin.
The Keystone discs are like 7/8" diameter when I first get them. You can use the ones from Sears or Dremmel that they sell anywhere, Lowes, Wal-Mart. I think they are brown. Those seem to cut faster for some reason but he Kestone ones are for dental. I just have a bunch of those. So many I'll not need to buy for a very long long long time.

But they wear down really fast and since I use them all the time I always have lots of them sitting in a bin that are like 1/4" or less in diameter. One of these used ones works great to just zip a head off a pin while minimizing damage to the sides of the recess it sits in or the surface of the folder.
The gold finish on that 560 is a bit of a concern for me when I do them and there is no way around that worry. I like doing it this way best of all the ways I've taken pins out and it takes a lot of patience and a steady hand but it can be done. I've even managed to swap out pivots on FRN folders with no visible damage this way. Keyword is 'visible' there.
Because the head of the screws I use are 3/16" diameter on most 2-56 screws there is a slight margin for error. However if you get pivot barrels in 1/8" size from Jantz supply the screws that come with theirs are 5/32 or larger in diameter increasing the margin even a bit more for you. This way the head of the screw can cover the minor dings that may occur around the pivot pin you are removing.
What I normally do is remove the head completely. Then sitting the body on a soft pin block with a hole drilled in it to allow the pin to go through on the other side I position the folder so I can tap the pin through. Sometimes it goes all the way through no problem. Other times it resists. At this point most always the head on the opposite side is sticking out far enough to cleaning zip it right off using the disc and then you can round the edges so its for sure going to pop through and you simply tap it through the other way.
Even though doing it this way has been successful for me I always warn those that ask me to do it to prepare for the worst. There is always the chance of a ding of some kind or another anytime you modify a folder. Just goes with the territory as they say. Fortunately for me its been less of that and more of the successful mods. Knock on wood.
You could always cover up a ding on the pivot like this hear too in the attatched pic. Just stick a clip over it.
Here are a couple of others I've done for various others or myself. Just in case you want to see it. The one pictured was mine I believe. At least at the time I did the work. At least I think that is the one I had. I may be mistaken. Anyway, if you look close you can see a small ding on it to the right of the pivot on the non clip side. I managed to reanodize it to match though.
http://www.bladeforums.com/forums/showpost.php?p=3916096&postcount=9
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