Why shouldn’t churches be allowed to endorse candidates?
Sorry it has taken me so long to reply; this is an issue that I worked on decades ago. Like you, I initially didn't like the Johnson amendment but, after doing some investigation back then, understood why it should be enforced. And it has taken me awhile to remember the various ideas as to why it is a bad idea.
I did somewhat remember the claim about how a pastor trying to promote a controversial candidate could split the congregation -- and I think it has some validity -- but it isn't really convincing. I also thought about how many churches take people to the polls, trying to ensure they get the vote out for causes they care about and how telling parishioners how to vote as they are dropped off at the polls on a church bus (something that occurs in the South) is a bad idea, in general. Sure, it is great if that church supports your stance but what if a Muslim congregation starts doing this, or a Mormon one -- and they support candidates that end up winning solely based on the support of that religion. But, even that isn't the reason, as obviously they should have the same free speech rights as any other church.
Of course, there is also the issue if the pastor is deceived by a candidate -- the candidate appears to be the perfect person for the church to support but (maybe a bit like Santos) you learn that this candidate went to different churches and told each what they wanted to hear -- that he doesn't actually support any of those positions. Or, that the candidate turns out to be a criminal who was engaged in actual fraudulent activity, maybe even some types of sexual sins, and the pastor is embarrassed because he was deceived. This is the type of thing that could kill a church.
The real issue is this -- it is easy to set up a church in the US. You don't require any actual "church" (the Scientologists are something of an example).
Another good example was John Oliver, who part of his HBO show, set up his own church to show just how easy it is to get tax exemption for a "get rich quick" scheme (preaching a prosperity type of belief). He didn't even try to hide that it was a joke, calling his church, "Our Lady of Perpetual Exemption." Despite that, and talking about what he was doing on his HBO show, he had no issue getting his "church" legally recognized as a religion. And before you get upset at the Federal Government for going along with a "fraud," realize that it is the fault of the First Amendment -- basically they have to recognize any claims of faith as valid to not violate the First Amendment.
This is why the Johnson Amendment makes sense and why churches should be in favor. The issue is, various liberal and/or atheistic groups could start founding churches (think George Soros) that aren't actually churches, they are "fronts" for political organizations. Basically, they could run a political group, which would typically be required to pay taxes, as a tax-exempt church. They could have "members" who they communicate with and "tithe" to the church that they send "sermons" to each week, have only "church services" where they preach their political gospel, etc. Without the Johnson Amendment, this church would be breaking no laws. So, you could suddenly have things like "The Church of Abortion," "The Church of Sex," etc. and nothing would stop them from being "religious" political action committees -- as you appear to think churches should become.
One additional note, why does a church need to promote a particular candidate? Churches are free to speak on political topics; they are free to preach against abortion, homosexuality, even things like power issues or nuclear weapons. In most cases, shouldn't the members of the church -- based on the teachings of the church -- have a pretty good idea of what candidates the pastor would support?
I support the Johnson Amendment because of the abuse that can, and likely will, occur if we don't have it. Additionally, I don't really think it is that limiting to churches, again, parishioners should be capable of knowing what candidate best represents their beliefs without a pastor having to point it out to them. The idea that you need a pastor to tell you who to vote for is demeaning to Christians.