Trying to eliminate Coccidia all together is all but impossible. It is a natural occurance and is always present. It is in you, me, dogs, cats, etc. the idea is to control it. Keep the enclosure clean and keep stressors to a minimum. A healthy animal will have low counts and will be none the worse for it.
I clean my dragons tank every week with a coccidial cleanser. I know that is not so easy in a chameleon enclosure but we have to do our best. I have never had a fecal that was entirely free of coccidia and don't ever expect to. If you are ever told there is NO coccidia present, ask what the actual count was. i promise it is NOT zero. The best we can do is ensure the counts are low and at harmless levels.