As far as I can tell, the Lord isn't working His will upon nations in this way anymore. The genocides of the Old Testament were usually wars which kept the nation of Israel preserved, either physically, spiritually or usually both. According to Revelations, there will be more wrath poured upon the world at the end of days, but not in the sense of Jephthah leading the Israelites against the Ammonites. The nation of Israel were not only God's chosen vehicle for bringing about His plan of redemption, they were also a nation in a very hostile environment. Take God completely out of the picture, and the Israelites would have still gone to war, or face extinction themselves as a nation.
So what is truly your question here, coelacanth? Is it whether or not Christians partake of "pick and choose" morality, with Jephthah as an example? Or is it that the genocide that Jephthah perpetrated upon the Ammonites, under God's authority and within His will is in of itself immoral and therefore an adequate reason to reject God altogether?
If your question is either the former or a matter of both, shall we consider the matter of Jephthah and his daughter closed? Because there really isn't any basis whatsoever to believe that Jephthah's vow or his execution of that vow were in anyway ordered or condoned by God and I have yet to see any Christian apologist, scholar or just plain schmo like me condone Jephthah's action. As to whether or not Christians "pick and choose" pet texts to propound and others to ignore, OK, I think any honest Christian will have to admit that happens all the time.
But if it's more the second question, or if you're in effect asking both, then we seem to have come to the same question discussed in the "Did Jesus Contradict the OT", that is, who gets to say what is moral and what isn't.
You might say that genocide is the worst possible immorality mankind is capable of. I might say, no, I think abortion is, because babies in the womb are the most vulnerable of humans. We could argue this all day long and in the end, how can you say your moral choice is any more correct than mine? The Hun who raped and pillaged in the 5th century might say that his moral view of the world is the correct one and that he was totally within his rights and even responsibilities to murder, maim and rape as he followed good old Attila. Certainly the Taliban feel that they are exercising the moral high ground when they stone a woman for speaking to a man she isn't related to.
Again, who gets to say what is moral and what isn't.
As a Bible believing Christian, I believe in God and I believe that God is the final arbiter of what is good and what is evil and who is acting morally and who isn't. And, the God of the Bible is very much a "You do as I command, and I will do as I please" kind of God. He commands what we are to do or not do, and He works His will as He sees fit.
Do you have to accept that? No. However, if God is Who He says He is, it doesn't matter whether or not you accept it or not. All humans can and do reject God for being Who He says He is.
But, if He is Who He says He is, and we reject Him, then we have to live with the consequences of such rejection. It can be compared with someone rejecting the law of gravity. Anyone can choose at any time to reject the law of gravity and decide that since birds, insects and other creatures can fly, it's unfair, even immoral to say that humans can't fly and therefore throw oneself off of the Empire State Building. Such a person can enjoy the freedom that flight provides and the exhilarating rush of air. However, there will come a time (rather quickly) when that person will face the consequences of their rejection of something that is what it is.
There are ways that one could disprove the God of the Bible. For instance, if we could see an instance in which the God of the Bible acted totally contrary to His own Person. Now, I know that atheists and other unbelievers like to pull out instances of genocide, or whatever to prove that God is acting contrary to His own Person, but unfortunately full study of the Scriptures always seem to be able to reconcile God's actions to Who He has revealed Himself to be.
For instance, the Scriptures tell us that God is love. However, the Scriptures also tell us that God is wrathful and vengeful. If the Scriptures only told of us the one aspect of God, that He is love, then there could be a case made for rejecting the veracity of the God of the Bible on the basis of the genocides that are described as happening under His will. But, sense the Scriptures also tell us of yet another aspect of God, that He is vengeful and wrathful, then there is no surprise when we see Him enacting vengeance and wrath upon a person or people.