Maybe have it be configurable in the options menu? Some additional options could be stuff like: pause at sight of enemy, pause when at 0 food, pause when at 0 money, etc. Things that could end your game, but which you can overlook if your attention slips for a moment. If implemented it should be fairly limited though, or otherwise it would break up the tense atmosphere you got going on.
Auto-pause would also almost be mandatory if plan on adding in an option to speed up travel time on the stragic map, because you could easily kill yourself or have no time to react to threats that pop up without it.
