If you want to make a Christian uncomfortable, challenging God's morality is a tragically easy way to do so. There are many things in Scripture we find disturbing, to say the least. This is something atheists, in particular, like to pick up on. They constantly point to things in Scripture which, in their mind, are evil. And as Christians, we strangely concede that territory.
This sorry state of affairs is degrading to God. It's as if He is our equal. Like when we look at an otherwise good politician and must overlook the times they inevitably drop the ball. Regardless of your opinion of Donald Trump, think back to his famous "grab 'em by the..." line. If you hate Trump, that's more ammo for you. Look at this pervert, you really wanna vote for him? If you support Trump, you might ask "man, why did you have to say that?" Then you explain why, in spite of that, you still support him.
But when we do the same with God, we concede too much ground to the unbeliever. We give their error credibility, and actually allow them to harm our own walk with God. We begin to think He genuinely is abusive, and that we even have the authority to judge Him. But unlike a human leader, like Trump, we do not. When we read Scripture and find something we don't like, or when someone objects to Scripture, and we think "man, why did God have to say that?", the simple answer is "because it's true".
God, you see, is the truth. When Jesus said "I am the way, the truth, and the life", He wasn't lying. This is the same God who, with nothing more than a command, created the heavens and the earth, and all that is in them, in 6 days. Everything you see before you, even the light by which you see it, is all a result of God's command "let there be...". So by what logic do His moral commands carry any less weight?
Let's put it another way: By what authority does one judge God? Ask any atheist to explain why God was wrong to do what Scripture says He did, to say what Scripture says He says, or to think what Scripture says He thinks, and they will stutter a highly flawed answer. And if you think about it hard enough, so will you. There is nothing that gives a man authority over God. No man can cite his opinions or preferences. No culture can argue from their traditions. No nation can vote Him out of office. No government can charge Him with treason. All authority stems from Him.
So what does that say about us when we disagree with Him? Simply put, it says we are...
Wrong.
We are wrong to suggest God's judgments are in error. We are wrong to suggest His punishments are too harsh. We are wrong to say His actions are questionable. We are wrong to say His commands are problematic. And we are wrong to let atheists say, much less actually make us feel, as if any of those feelings are valid.
Ultimately, therefore, we need to stop defending God as if He is our equal. When we defend a political leader, it is ok to suggest they are wrong, especially if they actually are. But when we defend God, we must give due attention to the fact He never is. Thus, it is not for His benefit, nor even for ours, that we defend Him, as if He even needed defending. Rather, it is for the benefit of the lost that we seek them. In time, every knee will bow, including the knees of those who so arrogantly call God's morality into question. Let such a sin be theirs alone.