But can you honestly say, that without the effort of Section 31 (
whether a private organization or not) that the forces of the Alpha Quadrant would have been victorious in stopping the invasion from the Gamma Quadrant?
Like it or not, the disease they spread into the Founder's species and the fact there was a withheld cure was the linch pin of victory. Maybe in time the combined force of the AQ would have prevailed (not definite), but it would have been a very different kind of AQ that emerged.
S31 actions were similar in some ways to the action of the Prophets in destroying the Jem'Hadar ships. An outside influence, one that none of the governments controlled. But whose actions were a positive contributing factor to the ultimate success of the forces the various forces the governments
did control.
Think of S31 Sci, like the two atomic bombs dropped on Japan, you don't have to like them, but you do have to acknowledge their results.