Assuming the fungus space travel and any other technological advancements shown during STD have to fail in order for canon to be maintained, Lorca and the Discovery crew will have to be defeated. My money's on Burnham being turned into some sort of evil destroying messiah / female black Jesus character as was done to David Tennant's Doctor by Russell T Davies. It's so obvious, and it will massively offend Christian white middle America, something which STD has been explicitly written to do.
Even the show doesn't manage to do that, the cast are already managing it in spades.
Speaking as White Christian middle America, I'm reminded of Gene Roddenberry's belief WHO WATCHES THE WATCHERS would be highly controversial and shocking to America when it turns out most Christians actually agree you shouldn't impersonate a god. Given so many review sites also see the Klingons coming off as ISIS and people just CONFUSED by the man children who think it's somehow more PC than regular Trek--I think the show will do fine.
I do foresee Discovery's first season ending with Lorca dead and Burnham as Captain, though.