By that point, the sphere was actively resisting attempts to tamper with it or delete or destroy it, though it doesn’t appear to have developed a personality.
They couldn’t just destroy Discovery?
They tried, in “Such Sweet Sorrow” - the sphere disabled the auto-destruct and raised shields, preventing the Enterprise from firing at Discovery.
Or spore drive the ship far away?
I believe they discussed this as a possibility in “Perpetual Infinity” - IIRC, their conclusion was that it was too risky to bring the sphere data anywhere, which was why their original plan was to “merge it into the river of time” (which, to me, suggests they never actually intended to leave the wormhole.
I don’t personally think the climax of season 2 is very good or clearly-written, but there are explanations provided for a number of things.