This has probably been answered but, I can't read the whole thread.
The Torah is based on G-d's Justice.
In this case, Justice means due process. You are not allowed to simply kill people or wipe out a city without due process.
So yes, this is different from "my god can kill more people than your god..." Or, simple conquests - "kill 'em all and take the loot."
These Commandments are directed towards the People of Israel who made a Covenant with G-d to accept G-d as their G-d. And, G-d promised that if they accepted Him. He would make them into a Great Nation and if they rejected Him, He would reject them.
However, in ALL death penalty cases, many things must happen before one is allowed to take another human life.
The person (or the city in this case) must be warned by at least two witnesses that the crime he is committing is punishable by death. The person must understand this commandment and penalty.
At least two witnesses must see this crime occur and be able to testify precisely how, when and where this crime occurred.
If any of these steps are not taken or are confused by the witnesses, there is no crime involved.
There is even doubt if the first time the crime is committed whether or not the person is liable. A repeat offender who had had the benefit of all of these previous steps would be taken to Court.
The Court would have to Judge the crime based on the testimony of the witnesses. If there were contradictory witnesses, the crime would not be punishable.
If the Court ruled unanimously that the crime was committed and the death penalty should be applied, the perpetrator would go free. Jewish Law demands that at least one Judge must doubt the guilt of the accused.
I am sure that there are other technicalities that I am leaving out but, that's basically it.
G-d's Torah was given to promote Justice as opposed to the self willed whims that rule Man on a daily basis.
It is very, very difficult to administer the death penalty under Jewish Law.