All three are wrong grammar. You must change "has" into "have, like you suggested.
As for the remainder of the sentence...
Option 1 is better than option 2. The word "whom" is smoother than the word "that", in that particular place - due to the complexity of the sentence, the precision of whom is appreciated there. But option 2 is not strictly wrong, it's just inferior - it's a more awkward, less clear way of saying it (between educated native speakers, at least).
Option 3 would be the clearest way to say it, of all three options, if only we replaced the comma with a dash or a period. As it stands, the grammar is so poor when using a comma there, that we can say option 3 arguably has the worst grammar of them all until this is fixed.
You are correct in guessing that "they" and "them" both refer to "others" in option 3.