They won't want to send a 1000 Cubes until the targets make themselves worth it
The Borg once sent a fleet to assimilate a world with a population of only 100,000. Were they more of a threat to the Borg than the Federation? Also, just because no other species have successfully used a virus-like attack doesn't mean it is impossible. For all you know, the virus the Enterprise crew came up with might have been radically different from any tried before.
Anyway, the Federation wouldn't pose much of a threat to the Borg if the virus could be easily contained by the Collective, would it? And once again, PICARD WAS SURE THE VIRUS WOULD WORK! If you thought you had a sure way to end the Borg, it would be ethically abhorrent for you not
to use it. Let's face it, PICARD WAS WRONG, there should have been a court-martial.