I'd be interested to know if the "safety concerns" are about the physical safety of the return vehicle, about the safety of the drugs, or political, but the article doesn't really get into that.
Asparouhov is quoted as saying in an interview in Ars Technica. “We are effectively the polar opposite type of re-entry vehicle. If those are luxurious limousines, we’re building like a 1986 Toyota Corolla that is meant to be less than a million bucks a pop, quickly refurbished, and then shot right back into space.”
I'd speculate it's about the physical safety of the return vehicle.
This appears to be the safety sheet for ritonavir: https://cdn.caymanchem.com/cdn/msds/13872m.pdf The lowest fatal dose in mice is 400 mg/kg, and the LD50 is over 2500 mg/kg. It seems like a fatal dose would present more kinetic danger than chemical. Plus the entire capsule is only 120 kg. Even if it were entirely made of ritonavir, and a single human ingested all of it, they'd have to weigh 48kg or less to hit the LD50. It is listed as being an eye irritant, but I would imagine so are half the chemicals in a spacecraft.
Sounds like they did plan ahead for if they were unable to re-enter after 3 months as originally expected.