I fear my games may contribute to both problems (merging two items, and adding a sitelink to the wrong item). Both are facilitated by identical names/aliases, and sometimes it's hard to tell that a pair is meant to be different, especially if you don't know about the intricate structures of the respective knowledge domain.
An item-specific, but somewhat heavy-handed approach would be to prevent merging of any two items where at least one has P1889, no matter what it specifically points to. At least, give a warning that an item is "merge-protected", and require an additional override for the merge.
If that is acceptable, it would be easy for me to filter all items with P1889, from the merge game at least.