If the Free Exercise clause of the First Amendment were to be made absolute, complete chaos could ensue. Think about what that would mean. It would mean that anyone could do absolutely anything and could claim that it was part of their religion. The government would either have to let it all go or would have to start deciding whose religion was and was not legitimate, thus defeating the purpose of having the free exercise clause in the first place.
Just to take two relatively plausible examples, the government would have to permit the smoking of marijuana and the institution of polygamy. The Rastafarian religion from Jamaica sees marijuana smoking as a sacrament of sorts. Some splinter groups from the Mormon church believe that polygamy (which the official Mormon church does not believe in) is appropriate. The government would not be able to ban these practices.
Now take it a step farther into less plausible ground. What if someone wanted to resurrect pagan religions and have human sacrifice? What if they wanted to hold sacred orgies in city parks? If the Free Exercise clause were truly absolute, all of these things and more would have to be allowed. This could clearly lead to chaos.