I’d strongly disagree. Nothing is being done to alter the body, one is only tracking what the body does, the way people trying to lose weight step on a scale. The thermometer is taken orally, just like when you are sick. I don’t know what is unnatural about those things.
You are most grievously wrong in suggesting that fertility is being treated as a disease. This is quite the opposite, actually. Our sexuality and fertility are gifts from God, and they are so highly valued, we do not abuse either of them with NFP.
Contraception literally means hindering the act of conception. Having relations on a day where the odds are low doesn’t really fall into this group, but taking pills, using spermicidal gels, etc certainly would.