It sounds like you don't like this solution, but wouldn't it be better to suggest a better solution instead? I'm sure none of us want them wasting so much time undoing bad merges.
About objecting to an Arborist Project, it's my understanding these are solely profiles that don't fit into any current projects. So if you don't want them in a special Arborist project, then users may start creating thousands of 2-to-5 profile projects, whose sole purpose is to block their being merged. That seems much worse than a single Arborist project.
I don't see a problem with the 5000 limit. Only the Arborists know for sure, but if they need more room, there's no problem creating an Arborist1, Arborist2, Arborist3 projects, etc.
Turning a different direction, why isn't the 'rejected match' functionality not effective? Are people really forcing a merge in spite of the profiles being marked 'rejected matches'? Perhaps then, there needs to be some enforcement muscle added to this feature. Such as, if a merge has previously been marked as rejected, then permission from someone higher is needed first, to override that. Or perhaps only disallowed if it's a rejected match and pre-1800, or some similar limitation. If there is some enforcement of the 'rejected match' marker, then no projects are needed.