It might simply take a new chip architecture, OS, and programming metalanguage. If the virus can't translate its wacky sentience to the new platform, the problem disappears.
Can it be that hard to design incompatible architecture and OS? I think not. Granted the cost of revamping computer tech throughout an interstellar culture is going to be bankrupting.
Otherwise, who's to say the Virus can't overlay its personality on the organic circuitry? It's just a different architecture.
For that matter, any AI (or lesser processing system) that is hard-wired would be just as immune to Virus. It wouldn't be that hard to make hard-wired navigation processors, astrogation databases, combat vector and targetting processors, etc.