I don’t think the freedom of religion argument has been used to defend pedophilia per se. Rather, it has been used to defend “supervisors” of priests and churches (in the corporate entity sense) against charges of negligent supervision, etc. where the higher ups were not aware of what was going on.
The argument, I believe, is that a civil (secular) court cannot pass judgment on the policies, procedures, etc. that form the basis of Catholic doctrine or the adequacy of those procedures. In other words, if a priest’s supervisor determines that the priest’s moral failings should be dealt with through prayer, meditation, and counseling because church doctrine teaches that this is appropriate, then a civil court cannot judge the adequacy of those procedures. There are a couple of cases where that argument has been made in sexual abuse cases, and I believe (but am not sure) that courts have rejected this argument where the higher ups were in fact aware of what the priest was doing. The cases that have established that civil courts cannot judge the adequacy of church doctrine, procedures, etc. are:
Gonzalez v. Roman Catholic Archbishop, 280 U.S. 1, 16, 50 S. Ct. 5, 74 L.Ed. 131 (1929)
Presbyterian Church v. Mary Elizabeth Blue Hull Memorial Presbyterian Church, 393 U.S. 440, 446-47, 89 S.Ct. 601, 21 L.Ed. 2d 658 (1969) and
Serbian Eastern Orthodox Diocese v. Milivojevich, 426 U.S. 696, 708-15, 96 S.Ct. 2373, 49 L.Ed. 2d 151 (1976)
The following cases involved sexual abuse by church officials–I have no idea of what the issues or outcomes were:
Schmidt v. Bishop, 779 F. Supp. 321, 328 (S.D.N.Y. 1991) (child sexual abuse claim against religious institution)
Roppolo v. Moore, 644 So. 2d 206, 208 (La. App. 1994), cert. denied, 650 So. 2d 253 (La. 1995) (adult sexual exploitation claim against religious institution)
See also L.L.N. v. Clauder, 209 Wis.2d 674, 689-90 (1997).