The thing is, as Hadriel has so astutely pointed out, there was a Christ in the Chrono world, and it was most certainly not Crono (I, for one, fail to see the connection. So he gave his life for his friends. Big deal. That's no different than a hundred thousand other such people throughout all of history. Say, for example, the one guy in the 1500s that, when the enemy encircled his company with spears, he charged them, and drove as many of them into him as he could, so that the others could escape. But that doesn't make him a Christ-like figure, does it? People see the self-sacrifice, and think that is all that Christ did. Well, unless Crono actually took the sins of all the world upon himself and, through his death, destroyed and made atonement for them, he has no similarity to Christ.) Anyway, Hadriel has said before that the doors to the cathedral (which itself is a uniquely Christian building) has crosses on its wall in the ending. Now, a cross is an ancient thing, but it is a symbol of death and suffering. To be used on such a holy place requires the crucifixion, and thus can Anno Domini and Before Christ be used.
Now, there are those that would maintain that it is since the founding of Guardia. But could it not be that the two years roughly coincide? Or, more likely, that people simply forgot the exact year of founding, and for simplicity made it coincide with that of Christ's birth (itself a mistake, since Christ was born in 4BC, I think - the one who measured the years made a mistake.) It's happened time and again. Rome was said to have existed from 753BC, I think it is, but realistically, there were settlements on the Palantine Hill in the 800s BC, and only myth dictates that year as the founding of Rome. Likewise with Guardia: after 1000 years, the exact year is almost irrelevant. Thus when at the fair they say it's 1000 years old... it might not be historically accurate, but it follows whatever legend there is concerning the founding. The point is, though, many people seem to use that measuring system, and it strikes me that the founding of Guardia is not universially monumental enough to be in such widespread use.
As for the system changing... well, if it is not the founding of Guardia, then Porre needn't change it. In the west, I think it has only changed a few times in 'recent' years (ie. since Rome). They measured since the rise of Rome until a relatively late time, then after went with since the birth of Jesus.