What future episodes established is perfectly relevant. Until you can prove that the virus WOULD have worked, you don't have the leg to stand on.
Based on the information available in the episode, Picard should have used the virus. There is no other way to interpret it. He had the opportunity to deal a crippling blow to a potential threat to the Federation.
"Our primary duty is to maintain life and safety of Federation planets.". That line was spoken by Matt Decker in The Doomsday Machine
. In I, Borg
, Picard violated that oath.