Nope, he didn't condemn anybody. If anything, he SAVED the Federation from immediate destruction. And his morality was correct as well.
So it's moral to stand by and do nothing while others suffer? Which is what this argument ultimately comes down to.
As it currently stands the Borg are a remote threat. But a threat that continues to test Federation defenses. So that does constitute them as an 'active' threat? I think it does.
Only distance seems to keep the Borg from launching an all-out campaign against the Federation at the time of "I, Borg".
From my standpoint using the virus is the "moral" thing to do. Sitting on a weapon that may essentially stop a "force of nature" from destroying civilizations is downright wrong. Of course nothing in life is guaranteed... so it may not work. But the distance that seems to keep the Borg at bay still exists