I am aware of the requirement on their website. However, from my personal experience, I had 4 LoR's, 2 science professors, 1 employer, 1 dentist. I am not religious so I felt like trying to come up with a letter from a spiritual leader just for the purpose of this application wasn't the best thing to do. The interviewer was one of the nicest and most down to earth person I've ever been interviewed with. The lack of this letter was never mentioned by him or admissions at all and I still got an acceptance.
I would say that you might not want to count on this requirement being waived, but I just felt that you shouldn't completely discount this school if you can't get an honest LoR from a spiritual leader due to lack of religious affiliations. The school left a very good impression and I wish people weren't so shy to apply to it based on their own religious beliefs (or lack thereof).
P.S. Another side note is that LLU had a requirement that all science classes be taken within the last 5 years of admission. Being a non-traditional applicant, my first quarter of chem was taken during my freshmen year, which was about 8 years ago. I asked if this would be a problem and they said that it's evaluated on a case by case basis by the dean. Again, it posed no problem so exceptions can certainly be made.