A Virus? i don't think that is logical, and realistically seen its impossible.
You are saying a human beings virus can compete with a multi billion gigahertz AI, its firewall and anti virus signatures?
By the time you have even established connection you would utterly swarmed by electronic attacks, by the time you get your finger to hit the first key on the keyboard your ship wouldn't be under your control anymore, by the time your finger comes to the 2nd key, your ship would blow up or vent all air , and you'd be dead.
I don't think the concept of an AGI really is very understood by all. Its a sentient being that resides in ALL machines at the same time. When you connect or have as much as a open wireless connection, it will instantly decode the cypher hack it and make it work for itself.
There is no way any human being, any human electronic or any human-based AI can compete with enemy self-improving self-replicating AI. That is why all ships - SEE BSG , need a full human crew, no connected networks, not even a SINGLE connected computer, even network cables emit electronic frequencies that can be read and manipulated without physical connection.
Logical seen, the AI in this game is playing VERY nice. If it would be a dick, it would hack your homeworlds networks and overload all nuclear/fusion generators, poison all food and water and destroy all production and electricity systems.
So Fly-By-Wire would work exactly as long as it takes the AGI to decode the cyphers, and then your ships wouldn't by fly-by-wire, but fly-by-AI. Trying to win against AI's with electronic gadgets is like trying to fight a fire in your garden with a nuclear bomb.
Basically what i am saying is this -
There are several gaping Plot Holes in AI War lore, and we need to fix it. If officially and lets consider that you are right - So parasites are in fact no parasites, but EW-Ships (Hackers) and they have no human crew, the first logical lapse is - that you are saying to overtake an ai with an ai virus. The only thing that'll do is merge the 2 AI's and what you get might be 10 times as dangerous as before.
Secondly, Fly-By-Wire would be via electronic signals the ai could intercept (so why does it not do it?) and block (doesn't do that either) it would just have to hack 1 ship you control, send a virus back to you and you'd be SOL (and your homeworld defenseless)
Third, how exactly do you propose communication by-wire over many solar systems? Why doesn't the ai simply install a signal jammer?
Ehm, you see, this is the kind of stuff i made this topic for.
The most gaping plot hole of all however, is that all ships of the ai,
are the ai An AGI Is not a disconected computer, it is abord all its vessels at all times.
There are no sub-commander AI's, the AGI sentience itself is everywhere at once.
Which is why the idea of infecting a single ship of the AGI sentience with a virus is absurd. You would always fight the central AGI head-on, no virus you could develop that the AI couldn't disassemble in a nanosecond.