We're now moving into a world where there are two different formats; Standard and Expanded. First up, they will want to keep the Standard environment fresh and competitive (and let's be honest, they print a ton of grass Pokemon every set that rarely see play, so FGP was a way to try and make them a bit more viable).
Secondary to that, the cards in Standard also become part of Expanded. If you take the approach of "don't print cards that will create broken combinations in Expanded", then you're actually crippling the Standard format as instead of only considering the most recent rotations, you have to consider all the way back to B&W, even when a lot of the time tournaments will be running Standard and don't care about the older cards.
So realistically, if TPCi are adamant about running both formats (and personally I don't like the idea of Expanded becoming a mainstream thing, as it sets a much higher cost of entry to the game for new players as they need to acquire the older cards to be competitive - but that's just my opinion), you need to have a ban list for Expanded to protect the Standard format.
Banning Shiftry in this case was the least intrusive way to fix the problem they had perceived. They clearly are happy to have other FGP based decks out there, and rather than cripple every deck based on that stadium, if they perceive a problem in the future (Forretress for example), they'll likely ban that card rather than FGP to ensure that they kill the specific problem deck rather than an entire subclass of decks.