You Can't Search What You Don't Have
Verse one is a little problematic:
And it came to pass after he [Alma] had made an end of speaking unto the people many of them did believe on his words, and began to repent, and to search the scriptures.Search the scriptures? What scriptures did they search? Considering that the preferred form of record-keeping according to this book is etching things into metal, I highly doubt that there were a lot of copies of the scriptures lying around. It's also my understanding that, archaeologically speaking, paper was far from ubiquitous in pre-Columbian America. And the printing press hadn't been invented yet, so mass-produced copies of the New Testament were a long way off. I doubt there were many copies of the scriptures available in a town as wicked as Ammonihah.
Saying that a large amount of people "search the scriptures" sounds a lot like something you would write if you had never lived in an age without easily printed books. It sounds like the phrasing you'd use if you grew up in a modern, literate, industrialized society and you had a copy of the Bible in your home. It doesn't sound like something you'd say if you were an ancient American prophet and you understood that the limited availability of the scriptures severely curtailed people's ability to pore over them personally.
We Need MOAR Witnesses!
Then we move on to the most controversial event of the Book of Mormon since Nephi cut off Laban's head.
In response to the waves Alma and Amulek have made, the Chief Judge of Ammonihah rounds up all their followers (including children) and throws them into a big fire. He also makes our two heroes stand on the sidelines and watch as all the righteous believers are burned to death. Amulek turns to Alma and asks:
How can we witness this awful scene? Therefore let us stretch forth our hands, and exercise the power of God which is in us, and save them from the flames.To which Alma shrewdly responds:
The Spirit constraineth me that I must not stretch forth mine hand; for behold the Lord receiveth them up unto himself, in glory; and he doth suffer that they may do this thing...that the judgments which he shall exercise upon them in his wrath may be just; and the blood of the innocent shall stand as a witness against them, yea, and cry mightily against them at the last day.If that isn't a load of bull, I don't know what is. God, who knows the deepest desires of our hearts, requires witnesses? He needs people to die so that his judgments will be just? Come on.
If your mind is made up to throw hundreds of people into a massive bonfire, you're evil. If God saves them from being burned alive, you're just as evil as you were before...and both you and God know it. Sparing all those people pain and death doesn't diminish the depravity of the Chief Judge's actions. And besides—how many witnesses do you need before it's enough to condemn the man for his crimes? After he throws one guy into the fire, he's a murderer. If God really needs a witness that badly, why can't he use the first poor schmuck's innocent blood as the evidence and let all the other people miraculously escape the flames?
So much unnecessary death.
The Chief Judge is an Idiot
Following that grisly scene, the Chief Judge does something stupid—he throws Alma and Amulek in prison. I have no idea why. He'd just murdered all of their followers. What's to stop him from murdering them too? Especially considering that, due to the public uproar the two of them had created, he probably had more legal reason to punish them than he did to punish all those people he just burned. But, like a poorly-written fictional character, he decides to imprison them. It's kind of a "No, Mr. Bond, I'm not going to kill you, I'm going to let you live so that you have a chance to escape my evil clutches and defeat me" moment. Alma claims in verse 13 that the reason they weren't burned with the rest is because their "work is not finished." How convenient.
He taunts them. He beats them. He starves them. He sends in a bunch of people to question them, but they refuse to answer. In his rage, he asks them: "Know ye not that I have power to deliver you up unto the flames?" In Alma's shoes, I would have responded, "Are you kidding me? I just watched you burn a few hundred of my friends in a huge fire and you're asking me if I realize you can burn me in a huge fire?"
The Chief Judge is an idiot. After all, he was a follower of Nehor, who was a murderer. Although I guess it's fair to say that the pupil outstripped his master on that one.
Violence is Next to Godliness
Finally, after "many days" of imprisonment and abuse, Alma prays for "strength according to [their] faith which is in Christ, even unto deliverance." That's when he and his sidekick hulk out, break their bonds, and scare the crap out of the Chief Judge and his cronies.
Oh, and also the entire prison is reduced to rubble and everyone dies except Alma and Amulek.
This story sends two messages. First, it's that God plays favorites. If you start messing with his chosen prophets, God will obliterate you. But if you start throwing the less important lay people into bonfires, he'll just let it happen so he can punish you for it later.
Second, it's that God isn't any better than that dick of a judge. The Chief Judge's body count is probably a lot higher (although specific numbers of the bonfire deaths and prison deaths are oddly absent). But the two of them did pretty much the same thing—they purged the opposition and they did it with theatrical overkill. They both left some collateral damage, too. The Chief Judge burned the believers' children and God killed everybody else in the prison who had no connection to the Chief Judge's crimes.
Who wants to worship a God that has so much in common with a despicable villain?