You might call Amoretti, in Oxnard, California who have a line of Absolute colors which include some oil based colors which they list as able to be used with chocolate, but I think the only natural ones in that line are orange and yellow. Their regular line has a few more natural colors-- a pretty nice green, a couple of reds, more yellow and orange, but since they are water soluble, I don't think you will be able to use them with chocolate. They might work to make decorations which you could use to add to your cake pops.
Amoretti is pretty good about sending samples if you are a business. The colors are expensive, but usually you can buy pretty small amounts of almost anything they carry. You can check them out at http://www.amoretti.com. They have been very patient when I've tried to work out product research questions with them, and they do have some flavoring and other lines which are natural so they are worth talking with. Maybe if enough of us keep asking for natural the market will respond. I already see a lot more product than was available 10 years ago.
I think that it may be a good point that most people who want cake pops don't care if they are natural. They would rather pay less and have their bright colored candy melts than have plain colored real chocolate pops, which have to cost more not only because the chocolate is more expensive than the melts but because the tempering time and the more delicate handling just makes the labor way more expensive. I think I've lost a sale or two due to this. Have you researched whether your potential clients really are out there? My experience is that I care more about avoiding artificial colors than most of my potential clients. I do use them, but in my mind there are lines I don't want to cross.... If you are going for a small niche like this, You need to be sure it is really out there.