It sounds like Tom and James have basically the same idea for our particular problem, which I would support: enable a warning in the merge script when incompatible types are detected. These would have to be encoded somehow though - presumably in the property constraints.
>Tom>>> For all languages except English, it's the protein Wikidata item [1] that points to the corresponding Wikipedia page, while for Engish it's the gene item [2] that points to the corresponding English article [3].I don't think that this is ubiquitously true, though it is true in many cases. This happened because the original imports from Wikipedia tagged the wikidata items about gene/proteins as proteins. We converted all the EN Wikilinks that we knew about programmatically but shied away from doing that for all the other languages.