I'm thinking this is going to be an unpopular opinion. But I think J.J. and gang were attempting to pay homage to TOS..a shout out if you will. I don't think they meant it in a malicious way or anything.
JJ and gang paid endless homage to TOS in the first movie. It was clear to see that. So, it's probably no surprise they do it in this one too. Personally, I can accept the idea that Spock warned them to intercept the Botany Bay as a way of preventing a potential hazard. But along those lines: was Khan the *worst* thing he warned them about? Doomsday Machine? Whale probe? Borg? etc...
Anyway, I only partially spoiled myself with this thread. I'm sufficiently happy with how this sounds like it's going.