If I had the command decision, I would have introduced the virus to destroy the Borg. Simply put, the Borg were hell bent on taking over the Federation. Their "assimilate at will" attitude does not leave any room for discussion. The only way to have peace with the Borg is to either be stronger and nano-probe invasion proof, or be inconsequential enough not to beckon their interest. If you're stronger, do you sit back and watch your weaker allies fall into Borg subjugation? I think not.
The Borg are a fascinating experiment in cyborg technology. If they had an "assimilate upon request" edict instead, perhaps it would be fine to work with them. Actually, THAT is the kind of virus I'd like to see introduced. The Borg shift into an assimilate when permitted stance and are no longer overtly hostile. And, they would also be staunch protectors of their allies, assuming a deadly invasion force ever comes about (like The Dominion).