Ritz has been going downhill since his Junior year of HS.
Yeah, that 12:56 sure was a bummer.
Anyways, I am not sure about the Achilles sheath, but it may have been an old injury he re-aggravated with the indoor session. Can't imagine one indoor workout wrecked a perfectly healthy Achilles. Remember, there are a lot of guys from the 70s who had to hang 'em up because of chronic Achilles issues, and Salazar knows many of them.
With regard to the neuroma (probably Morton's neuroma, if I had to guess), it is actually one of the few running injuries for which surgery is pretty much your only long-term option if early conservative care doesn't work out. Sometimes a nerve bundle gets thickened, and you have to lop it off. Unfortunately, there is a chance the surgery (which is literally just lopping off the thickened nerve) can itself cause more nerve irritation. Wikipedia says about 20% chance of recurrence.
But to be honest, Ritz is 28 now. He knows, and Salazar knows, that if there's a time to get everything in order, it's now. Realistically, he will probably be past his physical peak at 5k/10k by 2016, so it is probably worth the gamble to take the surgery option NOW instead of "take 6 weeks off and we'll see." Especially if he's had a neuroma he knows he needs to take care of--who knows what kind of burden that could impose long-term, if not dealt with?
Obviously, this is a shame, and another reason to question all these great runners hopping onto the Salazar bandwagon. But we need to remember that 1) Salazar DID lead him to his 12:56--even if you credit Hudson with the base to enable it, Salazar made it happen-- and 2) Ritz has not been the paragon of health and wellness in his years as a professional.