Student or Learner
I know the sentence without "who" or "whom" would be the most natural, but if we'd have to choose between them, which is more natural? I have a problem with "whom" there because the relative pronoun that should come between the parentheses should be an object for "I thought" but a subject of "proved to be a stranger".The woman (who/whom) I thought to be his mother proved a stranger.
The relative pronoun is the object of thought here. The subject of proved is the woman. The fact that you're telling us something about this woman through the use of a relative clause does not affect the relative pronoun's use in the relative clause. Seeing that it's an object then, whom should be technically correct in more formal English. However, who is rather more acceptable in everyday language, as well as grammatically acceptable. So I'd say you can use both, but who would sound more natural in contemporary English.