It was a problem back in 1948. That was when it was used to strip religion out of public schools. You may or may not agree with this usage of it, but the fact remains, that was not it's intended purpose when it was written.
That was a judicial overreach caused by a bunch of Roosevelt appointed Kook judges... and the horrible and overreaching manner in which that terrible amendment was written, and the vile and coerced manner in which it was passed.
It was not until 1962 with the Engel v. White decision