they had little choice. either they kill them or they die. sometimes you can't save everyone and you have to make a tough decision. it sucks but that's the situation they are in. plus the mind controlled ones would of died anyway without proper medical treatment. and they can't waste men to baby sit them. if they were better equipped or natsuno was helping then it wouldn't be as one sided. but as it is shiki are out to kill them and they have guns while the villagers only had wooden stakes. its also not like the shiki haven't been brutally murdering people either.