[Q]

"Now I'm busily editing my EVENTS and INTEL PROJECTS files to make as many parallels between Messages from events and intel projects as possible to make life confusing. Only when you see the 'We suspect the (name) empire of this act.' will you know it was an intel operation. Coolness!"

I think you can easily make the differentiation in the log file: just select "intelligence" or "events" and you still can determine, if it was a natural event or an intel operation.
But besides that great idea and good observation!