Pep has predominantly always been successful in his managerial career, at clubs which were already a success; even City was beginning to make some headway when he arrived.
That said, Pep has had that coaching gift, and the resources, to keep re-inventing, re-developing his team, moving players on, carefully nurturing younger ones and when necessary buying 'off the shelf' (so to speak) players who he knew he could integrate into his style. It is arguable also, that he has been able to get that extra 5% out of a large number of already recognised top players.
Even if City come out of this situation with their reputation intact, it's possible Pep will move on anyway, having done everything he could do with the club. If the clubs reputation gets tarnished, he will also still be likely to move on, in his career and his personal life.
In either case it may well be the case of 'shake the dust' etc. and move on.