also, i would like to point out we dont know what time scale the game is on. 3 hours could be 3 months for all i know. and 3000 would be adult male population most likely (to the ladies: men are more likely to be stronger, and in a pre-industrial society, strength is everything), so you have no idea how many children or women there are in the background. In 3 months, plenty of children could come of age.
Also, in farming societies, it paid to have about 6 kids to help do the work. Also, that 3000 does not count the population of the people on the farms, which are not included in the general population. So the actual population would be much higher. Militia probably grabs whatever is in the city at the time or something like that. In most agricultural societies, most people did farming, so if we say that 50% of the people are actually working on the farms, then there is a total of 6000 people in the city and surrounding area. So actually only 5.5% of the population would be killed. And that is on minimum statistics. Most likely, it is more likely to be higher than that.