I suppose L'Rell wouldn't just turn around and attack the federation because if the feds wanted they could port Discovery back to the planet and do some other damage if they needed to.
Enterprise shows up in the end, I would guess they were on the front lines the entire time, but their coms were breaking up, which either that was to mask the surprise for a little more until they showed the ship, or something fishy was going on there. Also the timelines are, Captain April 2245-50, Captain Pike 2254-62, War 2256-57, Kirk graduates from the academy 2257 but doesn't get the enterprise until 2265, in the prime universe anyways.
The spore drive is now offline until they can figure out a non human navigator, but in the prime universe it is never used again, so this is a loose end that needs tying up. I suppose next season will start their "5 year mission" of exploration.