A few things wrong with your assumptions. In the two examples you gave, God clearly says why he allowed the Israelites to drive out the inhabitants (clue: it's just the opposite of what you stated about the women and children). "Thou shalt not kill" is addressing murder. Someone taking a life into their own hands. But God is allowed to use death as a punishment given that we all already have that sentence pronounced on us due to sin. Thru Christ, God makes this right again by raising everyone good and wicked alike.
As for the serpent, the NT explains that by Christ Himself. The serpent was not to be used other than that one time and that was to LOOK at it, not worship it as an idol. However, because of the healing, it later became a snare to the Israelites and they did just that (worship it) and had to be destroyed. Likewise, we are to look to Christ one time for salvation, but not to hang crucifixes all over the place. I don't even have a picture of Jesus hanging anywhere as nobody knows what he looked like an such a picture would then become a form of idolatry. The Old Testament has types and shadow of things to come which was the case in this incident. Context is important.
