Two paragons can win alone, although it's much more reliable if you deploy additional stuff to clean up the second phase. For normal shielded ships, I find anything short of a very tanky capital ship just evaporates if it has to engage the dorito 1v1.
Your best bet is probably to spam squalls and a few Ion beams to try and lock them down at range and avoid fighting them up close.
You could also try to get ziggaraut which might be easier to do early, and then try to solo the doritos with zigg.
Maybe you could cheese them with afflictors too, but I don't play that way so I don't know if it's possible. I don't think the AI would shoot itself much though, you would be aiming to bypass shields with phase speed and assassinate them with anti-matter blasters. The fighters would probably murder afflictors though so I doubt that would work.