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Why do you want them to stop? They want to use Bitcoin and make an L2 on top of it.
No there is no way to make them stop with the current consensus rules and it's deeply pathological to even suggest such a thing. Bitcoin is supposed to be censorship resistant.
Another question: how many unprunable outputs are we talking about from Citrea? Hundreds? Thousands? Tens of thousands? Is this something really core to their business model
They need two taproot outputs to embed an extra 32bytes * 2 in. So in total they're embedding 144 bytes of data.
This is also in the worst-case scenario that's never supposed to happen, where the bridge is malfunctioning. In normal operation there won't be any data embedding here.