I never had this problem at all – I’ve never died because of the autopilot, that’s what it’s for after all.
Are you playing this on new windows versions or do you have a non-mainstream antivirus maybe?
When digging through the GOG forums I came to the conclusion that various security software like DEP on Windows or some antiviruses can prevent the I-War games from running properly. They just block some of the code by default and we end up with things like the well-known empty-menu bug and so on.
I’m sure that could also wreak havoc on some of the calculations ingame. Maybe try running it in compatibility mode for XP, disable the DEP and your antivirus. There are instructions in the help section here.
If it’s not that, I’m out of ideas.
Space. The final frontier.