I think what you're asking is whether their stay in the church was symbolic, and I would say yes it is. First of all Johnny was persecuted by his parents, but also by the Socs. It was this persecution by the Socs that led to Bob's death and caused the boys to run away. During this time Ponyboy and Johnny became closer friends and confidants.
Now, and here I'm going out on a limb, but think about these things:1)All of the Greaser's looked toward Johnny almost as a figurehead is he possibly symbolic of a messiah figures? His initials are JC. They do look to him for his gentle nature. They question whether they can go on when he dies.
If he is symbolic of a messiah figure, then yes the church would also have special significance.