Part of what enables pleasure-sex in humans is the fact that penetration does not trigger ovulation and that happens on its own schedule so evolution selected for mating strategies that would lead to frequent and short encounters. Additionally, the way we began to walk upright had the effect of moving human female genitalia more to the front which enabled her to be more selective about her partners. With the parental instinct being shared among both males and females combined with the fact both parties also are able to derive a great deal of pleasure from the experience, both sexes end up being more closely aligned with the goals of a sexual encounter vs those of our ancient ancestors.
To bring it back around, I understand what you are trying to say here, but disagree with your conclusion. Evolution selected modern humans to engage in sexual encounters that will not always result in a pregnancy, unlike eating which your body will always attempt to process the same as the last thing you are.
That's like saying that eating has been separated from sustenance (or nutrition) because people (just happen to) eat Twinkies for pleasure.
People doing something for reasons that just happen to not to be the primary purpose does remove the purpose of an action.