On the one hand, Destroy seems...more ethical. Wouldn't we all rather be dead than to live as somethingwe aren't? To no one's surprise, Jack prefers this to rewrite.

On a more practical side, more Geth who are now effectively Legion = more allies for you so that plus for using that virus.

This was my reasoning for my "canon" Renegade Femshep run
Just did Legion's Mission. A bit conflicted - unsurprised that Jack favors death over brainwashing. Me, I believe things like "Freedom" are overrated. The Heretic Geth won't even know they're different and in time, there won't actually be a difference. They'll be assimiliated wholly into Legion's camp.

That was what I thought though. I figure Shepard was more interested in having most of the powerful geth military on her side. Why destroy a perfectly good resource for no reason?