Well, if that's a concern he's too dumb to have his option picked up, especially since the second offense is a full season.
But I really don't think that's a big concern. The Phillies have history here. It's not like they cut ties with Freddy Galvis after his first failed test (and they even brought him back years later). And when Chooch got suspended that was actually his second offense (since there was no punishment for first offenses for that category of drugs). I don't even think he and the teams pursued a medical exemption subsequently. They also signed Marlon Byrd with a first offense hanging over him (and he eventually did have a second, much later).
JC Romero arguably was never as good after his 2009 suspension (which was for using in 2008). But that still might be the variability of relief pitching more than his baseline ability. Bastardo another one.
Kevin Frandsen was also suspended as a minor leaguer. Phillies actually had a ton of guys who were!