Luckily I was fairly close to this event in my current test session, so I now see what you mean with this issue. I don't get a CTD, but that could be related to vista being a piece of $hit.
I fought the defense of CdO, killed off both waves as well, and I got the attack repelled in the mission page before the battle with the second wave was even finished. I killed the last rebels and when I exited to the global map I noticed that the town was red. I could leave the area and go to Artrigo and get the reward. I loaded a save when I still was in CdO to check it out and I noticed a few guys wearing the "native" uniforms. I started killing them, and here's the weird thing, I din't enter combat mode when I did, they just stood there without responding. Once I killed them all, there were about five of them, the city was orange(neutral) and I could take over the city for myself by talking to the Mayor.
I checked the log while the game was still running, and the only thing that could explain this behavior is the old GUMID error. It seems the engine replaces a few rebels with other characters, in this case the natives, and that leads to unwanted situations like this. I've been trying to fix this issue for a long time but haven't been able to. I don't know if it's an engine limitation issue or something else I've done with the script. I've heard from my Russian friends that one shouldn't add too many new characters and I've added a lot, this could be the reason. I'll keep trying to fix it, in the meantime you will have to either load from a previous save and fight the battle again, or start a new campaign, I think that's the only solution right now.
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