The blood policy is a remnant of the past, a leftover of a time when they also didn't trust vaccinations, based on primitive fear and superstition. They would love to get rid of it, but it's difficult for them since they have celebrated individuals for throwing their life away by refusing this life saving treatment, so they can't now say it was all for nothing.
As a weasely compromise they give people an out by allowing factions. They know it makes no sense, that if blood transfusions were wrong (which is really not true and not supported by the bible) then fractions are wrong too, but they don't care, they will continue to let people die rather than admit they were wrong, just like they have always done, because this is an organization with zero integrity.