As you said, could be possible through worldgen event?
There was a mod for 1.12 that had the ability to disable specific structures by tapping into onChunkPopulate but that's probably changed by now I would assume.

@LatvianModder @MaxNeedsSnacks With the limited worldgen add and remove options for features, is there going to be a later implementation of this, or are we considering this implemented (at least initially)?

We're targeting a full worldgen rewrite for 1.18, so this should probably be kept open for now

That worldgen rewrite has happened, is this feature included @MaxNeedsSnacks?
(regardless of if KubeJS can do this 1.18's strucutre system can definitely do this, if a mod uses it properly)

Pretty sure Architectury didn't have the necessary hooks for me to do this (probably because Forge didn't have anything for it in BiomeLoadingEvent(?)) but I can check this out again for 6.0