The obvious answer to me is that Discovery exists partially within the prime timeline.
By which I mean the events of Season 1 happened generally as we saw them, but in the prime timeline the Klingons were normal Klingons using normal klingons ships to do those things.
Things get really complicated however when you throw Discovery Season 2 into things, because under Star Trek's own rule all the Wormhole based time traveling Michael and her mother did should have yeeted them into an alternate timeline ala the Kelvine timeline.
However we also know from Lower Decks that SNW exists within the prime timeline, as does Pike's time crystal experience. So either events went similar enough in the prime timeline that things lined up to have Pike end up with a time crystal even without Discovery, or there's a giant mess going on behind the scenes.
By which I mean the events of Season 1 happened generally as we saw them, but in the prime timeline the Klingons were normal Klingons using normal klingons ships to do those things.
Things get really complicated however when you throw Discovery Season 2 into things, because under Star Trek's own rule all the Wormhole based time traveling Michael and her mother did should have yeeted them into an alternate timeline ala the Kelvine timeline.
However we also know from Lower Decks that SNW exists within the prime timeline, as does Pike's time crystal experience. So either events went similar enough in the prime timeline that things lined up to have Pike end up with a time crystal even without Discovery, or there's a giant mess going on behind the scenes.