Slightly After-the-Fact Torah

I haven't commented on our Torah discussions for a little while. Though the meeting was Tuesday night, I can tell you what the group has been up to. I think partially I needed to mull over my deep disturbance about the parshot (sp?) we've been looking at.
The last few books of Numbers seem to be the root of several things about modern day Judaism that concern me. One of these is the history of Zionism, which tends to be all about excluding others and pushing them out of the land of Israel, despite the fact that they too have been there for thousands of years.
My parents were pioneers in Israel after WWII. My mother and her sisters came over from South Africa to help build the holy land into a home land for the Jews, and, at the same time, my father and his older brother came over. His brother stayed and returned only to work and earn money for his retirement, which he spent in Israel up to his and his wife's deaths, relatively recently. Their children were born in Israel, and, like him, returned to the US to work, but two of them soon came back to Israel to stay, and their children, whom I have not met, were born there.
I have never been to Israel, and though of course I am curious, I didn't especially want to go because of the stories my parents would tell me, about how, when the settlers began building kibbutzim, there were Arab houses full of things, food on the table, and the people just gone. Where could they have gone? At a very early age, I realized that those people didn't just run away when they heard Jews were coming. It took threats, and perhaps more, to achieve that result. And of course, I imagined myself into their position and asked my parents what right we had to take everything away from them. Of course they want to fight for their land; it is as much theirs as ours--perhaps more because we weren't there for so long, and perhaps, if the stories about being captive in Egypt are any example, since they are apparently fiction, perhaps we were never there at all, and this land just randomly chosen to be our hereditary holy land.
The sections of the Torah we have been reading lately include God's instructions to ruthlessly destroy every remnant (except virgin girls, who could then be made into breeders for the Jews) of the people then inhabiting the holy land. Peaceful coexistence was never a possibility. And people like Phineas, who skewered assimilationists in a bloody episode, were held up as examples. What does that make me, married to a non-Jew? Would I have been skewered too?
I don't like that racism or exclusionary strain in Judaism. It is what I rejected when I turned away from my cousins' insistence that non-Jews don't matter, and that American society has nothing to offer us as Jews. As far as they are concerned, we should return to Israel and stay there.
Also, the books we have been reading discuss Moses' last orders to the people of Israel, and the irony of these commands struck me hard. Remembering that Moses fled to the land of the Middianites when he killed a man in Egypt and lived there for 40 years, that he was married to a Middianite woman, and advised by her wise father Jethro, and that Moses' wife Zipporah saved Moses' life by circumsing their son, and was apparently sent away for her trouble, it was a shock to hear him order, with God standing behind him speaking in his ear of course, that all the Middianites should be killed, and that all their sons killed. How ironic is that? How are we supposed to feel about it, when this is the very story enshrined at the center of Judaism in the Passover story? Is it less unjust because Jews were the ones with the power?
I know my feelings are not unique among those in my community, but I still keep mum about them most of the time. But finding these things enshrined in the Torah shocked me, though I guess I knew that they were there, somewhere.