Good question!
It is a mitzvah on the witnesses to carry out the execution. I am unsure if the requirement is on them personally. Perhaps they can send an emissary.
If they refuse to even be nominally involved in the execution, it is possible that the criminal would be released. I assume that the din of ‘the walking dead’ would apply. This does not seem to be a reason to retroactively negate the testimony.
I would not consider their defiance as challenging the bais din. Rather, it is an unwillingness to perform a mitzvah. I doubt the rule of makkos maardus applies to communal mitzvos. So, the only consequence the witnesses face, is being called reshaim, by denying justice. The same as a witness who refuses to testify.