Well, the UFP doesn't use the Spore Drive incorrectly. Mushroom civilizations are safe now for the most part, and as far as the multiverse is concerned, I think that's safe considering that they only use it to get around places (so they coast the network), technically speaking, lets give Starfleet a little bit of break here.
The possibilities with spore drive are quite extensive, but realistically, they've just started using the thing (time frame-wise)... whereas the Voth and Borg both had TW capabilities/experience for a LONG time (centuries).
Considering Starfleet (or more to the point, Discovery) has been using this technology for roughly 3 years, I think they're doing alright.
Plus, Starfleet/Federation with 32nd century knowledge would easily be able to make using the spore drive easier, safer and make sure that it doesn't do any harm.
Plus, we don't know whether TW also causes untold extinction of subspace civilizations or damages the multiverse - thus far, we hadn't.