Center of the galaxy was definitely crappy planning.
The chief complaint, IINM, is that the Enterprise (and the BOP) shouldn’t be able to travel that far in any reasonable time period.
That point could have been addressed with some technobabble about a wormhole (possibly an unstable wormhole, adding urgency to the mission) or a technological solution like Barclay in The Nth Degree. Although it might have helped from the perspective of nitpicking geeks, mainstream audiences would likely find have found it pointless and perhaps alienating. That may be why Shatner decided to ignore the pickable nit.
Good call or bad?
I think bad call. You're right that it's an easy fix, just have Sybok discover some wormhole that leads there, like you say. When the script neglects things like that, it just comes off as either sloppy or lazy.