So just don't do that, the Flood probably wouldn't bother taking over trade ships anyway, since they would have a relatively small crew, and would be a waste of time and resources.Also the Flood wouldn't be using trade routes or refineries anyway, since they don't have any incentive to preform the menial task of transporting goods (and the Flood don't buy things, they are a parasite)They would probably need their "Credit" resource replaced, I think i saw someone mention people, which really could make sense, they keep the humans alive and then harvest them when they need more units. (oh my god that really did make sense =O )The Forerunners AI are also more like a Virtual intelligence, than a Artificial one. They have the appearance of thought, but follow the orders given to them by an actual AI (like the monitor) the Sentinels in the game and in shadow's of Onyx all follow the orders laid down by the Forerunners (in a way the Monitors do this too, but seeing as 343 sort of went insane, they must be AI) The Sentinels only goal on Onyx was to defend the Dyson Sphere. (is that right??[the Dyson part]) So the Forerunners dont really make sense.
In their war against the Forerunner the Flood took control of ALL ships, even ones with virtually no crew. Because, while the ship wouldn't be usefull to them for the sake of bio-material, it did provide a means of transportation. And even if those trade ships have little to no crew, they CAN go to planets, and so they can transport flood spores. And so like I said, implementing them CORRECTLY would take a lot of work. If you skimp out and make them no differant then the other races, then sure it can be done. But they wont truely be the Flood then.
As for the Forerunner AI, they work just as much as the Flood do. While their units (Such as Sentinals) aren't AI, their controlers are. Mendicant and Offensive Bias were both AI's, Mendicant was lured to the Flood side by Gravemind, while Offensive was tasked with stopping Mendicant. It's all laid out in Halo 3, at the Forerunner terminals. So if they were added, the Forerunner fleets would be used, and while those have no sort of intelligence, as they are crewed. They can also be tied to an AI, much the same as UNSC ships. So saying the player is actually an AI, like Mednicant or Offensive Bias would work. The player, the AI, would be controling the fleets of forerunner ships.
Both are plausible, one is easier to implement in terms of game engine, one is easier to implement in terms of ship designs. But both are perfectly plausible if we step outside the realm of Canon.