Well, what does the term "war" imply? No large group fights just anywhere, they fight on a battlefield. Battlefields are OUTSIDE cities, ususally far away. If a little group is in a war with a large guild, then it'll stay inside a city. Also, remember that the Cold War tought us that fighting is not just physical. A small guild might be able to convince people not to trade with members of a larger guild. Or maybe it'll sell things for lower prices than the larger guild. As the boycott of the large guild continues, guild members leave. Eventually:
A) the once-large guild is small enough to take on
-or-
B)it'll surrender
Either way, no fighting. Also, new things could be employed, like bribing guards to attack members of a guild, or poisoning a guild's stalls. Who knows