A societal emphasis on conformity can be useful. People who value conformity will quickly take up and adopt the norms. People who don’t particularly care will tend to conform mindlessly, because nonconformity is costlier. The only rebels, then, are the people who sincerely value nonconformity. Thus, an environment that rewards conformity makes it easy to identify those who don’t wish to conform.
A societal emphasis on nonconformity, however, doesn’t lend itself to identification. Conformists will conform with society’s standards and will go along with the crowd by ostentatiously not going along with the crowd, at least in a superficial sense. In such a situation, the only people who will stick out are those that wish to conform, and who reject the norms of a wider society. (For example, the Amish are conformists, but to a different standard than the societies that surrounded them; their rejection of those societies can be considered nonconformist only in a limited sense.)
If you want to work against the ingrained tendency of human beings to conform, you need to identify the people who lack that tendency. The best way to do so is thus to foster conformist in society.