This is a letter that I wrote to a friend who is leaving behind the Christian faith. I hope to begin a dialog with her, and may post excerpts from as we progress.
First, let me say that you're asking a lot of really good questions. These are the sort of questions that all Christians should be asking. But I should point out that how we ask questions determines a lot of whether we actually find answers. So, for instance, if I ask you something like, "When are you going to quit beating your wife?" I've boxed you in to a particular corner that there's no escaping from. Either way, to answer the question is to admit to beating your wife.
To be more precise, there are questions that come from a posture of faith that are earnest questions. They recognize that the problems are hard, but because they are approaching the question from a prior commitment to a set of beliefs, they may accept a certain amount of ambiguity--or better, wait longer for a clear answer--than someone who is asking without that prior belief. For example, because I believe that Jesus Christ is Lord, I am able to recognize and inquire about the problem of genocide in the Old Testament. But because I believe that and have lots of good reasons for believing that, I might be less affected by my lack of an immediately obvious rebuttal to the problem than someone who doesn't have the prior commitment to the Lordship of Jesus.
All that to say, questions simply aren't neutral. How we ask them matters considerably.
There's one other implication of this: I take a long view of faith and unbelief. I didn't wake up one morning and begin to believe that Jesus died for my sins. There were lots of factors, lots of experiences, lots of reading and searching that led me to that conclusion. I would expect something similar for going in the other direction. There is a lot at stake on the questions that you are asking: patience and diligence can be helpful tool.
That said, let's do this: rather than address all the questions you have raised here, let's just take on one, attempt to treat it with the depth it deserves, and then move on. I suspect many of the questions are overlapping, but that means as we get deep into one we'll get deeper into the others. I envision a long conversation here--weeks, months, doesn't matter. The advantage of email is that the conversation exists over long periods, so long as the Lord gives us both many years.
Let's start with the question of God's relationship to war in the Old Testament, as it clearly has ramifications for the unity of the Old and New Testaments.
First, I think that there is a question as to how we describe what happens (and here I think primarily of the book of Joshua). Is it genocide, or corporate capital punishment? It's important to read the text closely here: the Lord doesn't just command Israel to wipe out a people group. He is, it seems, executing a sort of corporal capital punishment on the Canaanites for their sins.
Consider: in Genesis 15:6, it is suggested that their sin "is not yet filled up." The book of Joshua happens some 400 years later, which is a considerable amount of time to put up with the sort of rank wickedness we barely have words for--child sacrifice, incest, bestiality, etc.
Second, Deuteronomy 9:4-5 suggests that it is precisely because of their wickedness that the Lord drives them out--not because he has "played favorites." Indeed, when Israel failed to drive them out completely, it led to the prophetic judgments against them for their own (similar) acts of wickedness. So in Jeremiah 23:14, God will say that Israel is "like Sodom to me." That's pretty strong language, and suggests that what's going on is not about war per se, but rather about sin and wickedness.
Now, this is only one component of the presentation of God in the Old Testament--and it's worth comparing this record to the book of Jonah, where God specifically sends warning to Ninevah to repent, warning which is effective. But it suggests that there is a fundamental conflict between sin and purity, and that the two cannot ultimately dwell together.
Your question, I suspect, is whether this is maintained in the New Testament. The answer is yes--and no. Consider: in the Old Testament, there is no distinction between the religious functions of Israel and its police functions--or, we might say, between "church" and "state." The New Testament, on the other hand, shifts the ground on this point by drawing a distinction between the state's functions and the church's. What does that mean for understanding the situation in Joshua?
Romans 15:4 suggests that what was written in the Old Testament is "for our instruction"--that is, for the instruction of the redeemed people of God who are constituted by the word of Jesus Christ. Under this rubric, Joshua seems like a foreshadowing of the eschaton--of the last days, when God will complete the work that Israel failed to do (eradicate evil and bring us into the promised land). That is, Joshua points us toward the final judgment.
Additionally, it might suggest that the state still has the role of pursuing justice within the temporal realm. Here again the distinction between church and state in the New Testament matters. The church doesn't abrogate the functions of the state.
Either way, the popular notion that God capriciously kills a lot of people simply won't stand up under a close reading of the actual text. There's a lot more going on than that.