That's not really my teritory, so bear with me. But isn't the idea of natural fermentation that you leave the juice/wort exposed to the air so it can pick up the yeast? Or do you rely on the yeast to be already in the juice?
It's acually the wild yeast that grows on the skins of the fruit that is relied on to ferment it when you go 'natural'. Basically you mash the whole fruit (unwashed and pesticide free) - Then you seal it as normal to stop any further airborne yeasts/nasties getting in.
No sweat! Just be sure that everything is sterile and dry. And I mean everything!
As long as the cider was not pasteurized, it will ferment. Be prepared to wait a week or more to see any action in the airlock though, it takes awhile to get going.