Contrary to common belief, Insurance is *not* healthcare. It's a way of distributing risk. For example, your car insurance will not cover oil changes, or regular maintenance. H*ck, even extended warranties will not cover those. This is because the cost structure is very well known (so and so much every 6 months).
Thus -- ignoring what these churches ask -- the only reason for including contraception would be reducing future risk. I.e.: the cost of these pills are well known, and the insurance would normally prefer not to cover them, as they do not cover aspirin, or baby diapers. However by including cheap contraception pill they mitigate a more costly future risk (a "cheap" delivery will cost 10K+ these days, and God forbid if there is anything wrong probably in the 100ks). So for insurance it makes sense to include these pills (still no aspirin).
However the church -- or whatever organization that does not want to provide these, just needs to have a separate pool of insurants, so that the cost of delivering a baby is only distributed among them. (I'm assuming they would also like to have more babies in general, but this might not necessarily be true for all religions).