It just takes longer and you may break a trace or two.

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You had better stress that "may" there buddy.

If you use a standard soldering iron, you should be using a 35W iron or better. I wouldn't do the job with a 25W iron myself. You will then need to apply heat to one side of the SMD cap, then "flip that side up in the air" when you've applied sufficient heat. Then you have one side of the SMD cap hanging in the air with the other side still soldered. Desolder the other side and you can remove the cap. But you will put strain on one trace when you flip the cap up, which is why it's always best to apply heat to both sides at once.

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Or you can use desoldering braid on both sides to significantly reduce the solder there if not remove it completely aside from a thin coating(less solder = faster to heat up and weaker). Then with much less solder to deal with often just flipping the iron between the two joints works well or on some occasions just heating up one side and even very slightly pulling can break the other joint. Since there is less connecting it there is less strain on the pad as the remaining solder flexes more easily.
When I started I did it more like you mention JDW and I had a good success rate until my cat ended up surprising me and I lost a good 1CM of trace while overclocking my PDQ (my tweezers were on the resistor)( I was able to fix it.. used a tiny strand of wire that I pulled from the wire left over from an old set of headphones.).

Since I started doing things differently I would be willing to bet that if something was to surprise me like that again I would most likely not loose any pads or traces.

Oh, and I was (and still am) using a Weller WTCPN with TC201 pencil and PTA7 tip for jobs like that. It works well and I like it. I also like how it is not very ugly and is all one unit. (datasheet here: http://www.divshare.com/download/2469822-98b )

Heh, I only recently made the jump to non-lead based solder and I am not entirely happy about it.

And no! I have not burnt myself yet.