Proving it would be problem given Lovok managed to avoid whatever anti-Changeling measures were in place at that point. Both ultra-paranoid groups with no love for Starfleet also are unlikely to take anything Sisko says on face value, so even if he warns them they might see it simply as Federation interfering in a matter that they see as no concern of the Federation (military action by a foreign power on another power outside of Federation space).
Starfleet would probably do pretty much the same as it did in the episode - nothing. While in the episode they don't want to interfere as the plan might succeed, in this case while they know if Sisko is right the attack is destined to fail but the Obsidian Order and Tal Shiar are fairly hostile towards the Federation and troublesome, so I doubt they would be in a rush to save either group. They might see it as good for the Federation if the Order and Tal Shiar were seriously weakened or destroyed. Sisko would still go off against orders to save Odo anyway.
Also given that Sisko and co don't know about the fleet until it is going through the wormhole learning it is flying into a trap after the fleet is gone and well on its way to the Founder's homeworld even if Sisko wanted to warn them he simply might not have the time to do so.