The incident may have darkened his soul, kind of like killing Cora darkened Snow’s soul. This didn’t change who Snow was she was still a good person. The difference between Rumple, Regina, Hook, and the rest of the villains is that they continued to do things to darken their souls knowing the consequences of their actions. They made a conscious decision to continue their evil ways. Bae on the other hand was not making a conscious decision to be evil he was being influenced by the dagger and once that influence was taken away he was back to being the really good person that we know he is.
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