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The meeting could determine whether the two young siblings would keep going blind. The doctor knew that going in, but he was feeling good. He’d negotiated huge discounts before, allowing patients to get complex surgeries or budget-busting drugs they otherwise couldn’t afford. And his last two conversations with Spark Therapeutics had been promising.

Then again, at $850,000 a person, Luxturna was more budget-busting than just about any other drug. Spark had proposed a few different ways of helping insurers to cover the gene therapy — but Dr. Kevin Strauss’ patients tend not to have insurance. As the medical director of the Clinic for Special Children, on the outskirts of Strasburg, Pa., he mostly sees members of the Plain community: Old Order Amish and Mennonite families, who believe that caring for the sick and the elderly is a community’s responsibility. Relying on governments or private companies to step in is considered a serious moral breach. They don’t want medicine for free. They just want to pay the reduced prices that government and private insurers often do.

That’s the kind of discount Strauss was...