Well the Imperium has many options available to it when performing Exterminatus. The word isn't a reference to a specific method of destruction brought down upon the world, but am archetypica action.
From the myriad sources found in the fluff, it appears that a fleet isn't really necessary, it just makes things a lot more expedient and certain to kill everything. We only have to look at the case of 57-Izar, where they hit the major population centres of the Saruthi with orbital strikes, then virus bombed the planet, and then nuked the planet.
While Istvaan was just some virus bombs, by multiple ships. But considering it's an airborne virus that kills anything, I don't even think a flotilla is necessary, if you launch a high enough yield in to the upper atmosphere where it can rain down on a large portion of the planet, and be carried around by air currents. And that alone would be enough, since only those things living in the deepest caves or parts of the ocean (or sealed bunkers) would have a chance of escaping contact with the Life Eater virus.