I gather the Iconian weapon was designed to countermand countermeasures, to defeat attempts at erecting a firewall, and (as we see from its deployment mode from the probes, and from the jump into Data) even to hop across actual physical barriers with relative ease.
The measures suggested for preventing infection would have been prudent, but I doubt they would have been completely effective. Remedial measures would also have to have been taken eventually.
I guess it's possible that a merely partially successful entry of the virus leads to an only partially successful infection, and the virus cannot reach its full destructive potential unless it arrives whole and undamaged. But it's also perfectly plausible to assume a viral program that can grow into a deadly "adult" from a teeny weeny fractal component and then make its assault. Unlike the Borg, who act like a force of nature and thus always seem to settle for the barely adequate, the Iconians would have been thinking in terms of humanoid guile, and would have built their weapon to provide absolute overkill against the starships of their enemies.
"Safing" the ship by venting antimatter sounds like a good idea - until you remember that faults in the antimatter handling system were the virus' chosen means of killing the Yamato. A complex purging operation might go horribly wrong even in the best of situations, and more so if supposedly inviolable components were compromised. And this would be basically the only thing our heroes knew about how the starship-killing threat worked... So they'd probably steer well clear of touching the antimatter if they could avoid it.
Timo Saloniemi