Your choice. The Cardinals never expected to put Flaherty on the 60-day injured list until they know he won't be back for two months. They don't know this at the moment. That's partially because he's only now starting his throwing program, but also because they have to see how his arm responds to treatment.
If there's anything that I can pass along it's this: Injuries can be hard to diagnosis. We, as media, should not oversimplify this by playing doctors in print. There are many examples of teams who believe a pitcher is dealing with something, but the root cause is another injury that is spotted along the way. Treat one, another emerges. Also, surgery is not the fix-all, cure-all, surefire answer. Surgery is to be avoided. You can probably mention dozens of pitchers who have returned from Tommy John surgery and not to many that haven't. Which is the point. It's not 100% effective. It's a remarkable surgery that it's close. But you don't remember the names of the pitchers who weren't able to regain their form because of just that -- they weren't able to regain their form. Surgery is meant to be avoided, and sometimes you'll see treatment plans and diagnoses done to avoid surgery for as long as possible. That's not because surgery isn't likely or that the injury was underestimated, they just want to try all alternatives first.
I'm not saying that's the case with Flaherty. I'm just trying to pass this information along because I hope that it's something I've helped readers understand with my coverage.