The quote is:
But we should have been wary of answering back (to the questions of aliens), until we have develop a bit further. Meeting a more advanced civilisation (aliens from other planets), at our present stage (at the current stage of the human beings), might be a bit like the original inhabitants of America meeting Columbus. I don't think they were better off for it.
In the last sentence, does the pronoun "they" refer to all humans? or "original inhabitants of America"?
Stephen Hawking WARNING: Aliens could DESTROY us if we find Them, an article from the UK - Express
I believe your sentence "Hawking doesn't think (the fate of) humans will be better [off]" by a visit from aliens is correct. Hawking was part of Breakthrough Listen – a group similar to SETI in the U.S. which scan the stars in the hope of receiving a message from space (aliens). “But we need to be wary of answering back until we have developed a bit further" and are prepared (defense etc) for a visit. He compared how the native American were overrun by the arrival of European explorers.
The "they" Hawking refers to is the native Americans, not humans. I agree it's a little ambiguous but given the placement of the sentence and the fact it's in past tense there's enough evidence that Hawking is not referring to a human encounter with aliens since purportedly, that has not yet occurred.
