I am a Christian and I was wondering how we deal with the question: "How can God command us not to murder when God murdered sometimes mass amounts of people in the Old Testament?"
You're having difficulty understanding this because of your imprecise usage of words. God, in the Bible, makes a strong distinction between killing, accidental murder, and intentional murder.
Murder is something that is easy to understand as being wrong. God has always opposed murder. It is listed as one of the things that God finds abominable in Proverbs 6:16-19. The word abominable has an interesting meaning; it literally means something that makes you sick to your stomach. God is not a physical being who has a stomach to be made ill, but the word conveys the idea that God finds murder a disgusting concept.
Many sins that men commit carry appropriate punishments for the sins. Even before Moses brought the Old Law to the Israelites, God gave mankind a command that murderers were to be put to death (Genesis 9:6). Some people think that killing murderers, called capital punishment, is a silly holdover from more primitive times that modern, civilized people should no longer practice. However, since God has commanded capital punishment, it would seem that a culture that does not kill its murderers shows a disrespect for the wisdom of God.
To some people, killing a murderer is just another form of murder. To these people any taking of a life is wrong. Often, Exodus 20:13 is quoted, "You shall not kill." Some translations do render this verse in this way, but most good translations render the verse, "You shall not murder." The Bible makes a distinction between killing and murder. Obviously, from Genesis 9:6, there are times that killing must be done.
In the same Old Law that gives the commandment to not murder, a distinction is made between premeditated and accidental killings. See Exodus 21:12-14, 29 and Deuteronomy 19:4-6. Premeditated murder was punishable by death. An accidental killing was not punishable by death.
Under the Old Law, the nearest relative to a murdered person was assigned the responsibility of seeing that the correct punishment was given to a killer. This person was called the avenger of blood. Obviously, there is a possibility that the avenger would not be totally impartial in the choice of punishment. However, he would be strongly motivated to see that some sort of punishment was carried out. In our society, a prosecutor would be equivalent to the avenger of blood.
To balance the possibly overeager avenger, God established cities of refuge in the land of Israel. If a person accidentally killed a man, he would immediately run to the nearest city of refuge. The idea that if he did not get there soon enough, the avenger could justifiably kill him served as sufficient motivation for a person to turn himself in. In this manner, the Jews were able to function without a police force.
Once the killer reached the city of refuge, the judges of the city would try the person's case. The avenger would serve as the prosecutor and the killer would be his own defense. The judges would establish whether the killing took place if the man had done the killing and whether there was prior hatred between the killer and the victim. If there the later was true, then it was assumed that the killing was premeditated murder and the killer was put to death outside the city. If the judges determined the killing was accidental, then the man had to remain in the vicinity of the city until the current High Priest died. In other words, accidental killings were punished with a form of imprisonment. If the killer left the vicinity of the city before the High Priest died and the avenger happened across him, the avenger could kill the man without penalty. In other words, the Israelites had prisons without walls or guards, yet they were just as effective as our modern prison system. See Numbers 35:15-34 and Deuteronomy 19:1-13 for a discussion of these laws.
Murder is wrong when innocent people are killed. It is wrong when a person is killed without a justifiable cause (I Samuel 19:5). It is wrong when a person is killed out of hatred (Exodus 21:12-14). Even governments can be guilty of murder when they allow innocent people to be killed within their borders and not extract proper punishment (Joel 3:19). Sometimes a government is even involved in killing innocent people. King Manasseh had many innocent people killed during his reign in Judah (II Kings 21:16).
The wicked are quick to shed innocent blood (Isaiah 59:4-8). After the deed is done, they try to cover up their wickedness or to justify themselves. Some will go so far as to pass laws to justify their slaughter of the innocent (Psalms 94:20-21).
Of course, Christians are not to practice murder. Remember that the difference between accidental killing and murder was whether a person hated the victim. In I John 3:15, Christians are told not to have hatred for their brethren. If you love your neighbor as yourself, then you will not commit murder (Romans 13:9). If you must suffer at the hands of a government, then you should suffer for being a Christian and not for a legitimate reason, such as for murder (I Peter 4:14-16).
While we are on this topic, some people wonder if killing in war is against God's law. Once again remember that God said that murder was wrong. Some killing, at times, must be done. When two countries fight, it is rarely because of a personal hatred between the two armies. There is often a general hatred of the enemy, but not on a personal level. We also cannot claim that innocents are being killed when both sides take up weapons to fight, though the killing of innocent bystanders would be wrong whether a war was going on or not. Throughout the Old Testament, God calls on the Israelites to take up arms against a nation. Sometimes the battles were in defense of the nation. At other times they were sent out by God to punish a sinful nation. In either case, killing was done with the approval of God. Hence, we must conclude that killing in war is not considered murder and is not a sin. Even in the New Testament, wars are not condemned. Often soldiers and their equipment are used to illustrate points in various lessons.
Your question though asked whether God murdered people. The answer is no. An innocent life was not taken by God. People, and sometimes nations, guilty of extreme or extended sin were killed, but this was not murder but avenging the wickedness caused by these people or nations.
Some people have a strong objection to any sort of killing. It is not wrong for them to follow their conscious and to avoid all violence by their own hands. However, at the same time, they must understand that they cannot impose their views of non-violence on other people since God has authorized some violence in certain situations.