Blame Roof for this mess, not Apple
If your boy Roof hadn't been shown waving some damn Confederate flag and then gunning down innocent citizens, this banning of the Confederate flag from games nonsense wouldn't have happened. It's obvious no one close to you was killed so you can take a nice comfortable view of the situation. However, more sensitive people feel they have a need to do something even if it is futile or doesn't make much sense to you. I think they're trying to defuse a bad situation. Any fool knows that displaying a Confederate flag isn't hurting anyone but now they suddenly see some connection between the Confederate flag and racial killings and for the time being it has to be shown that people care about what happened. I would think Apple might have received some heat to pull those apps or they simply went along with other companies out of respect for the murdered victims. When it comes to human emotions, things don't have to compute, as you put it. Not all humans are as rational as you are. Their feelings tend to get in the way of their judgment. They're not machines, precisely weighing out every little factor. In this situation, not everyone can be pleased.
I'm sure in the future you'll be able to pull out your Confederate flag and display it proudly like your forefathers did but for now you'll just have to be patient until things cool down. I'm a Northerner so I never waved a Confederate flag and it means almost nothing to me if it's removed. I just view it as some old flag of a long-dead Confederacy. I never met anyone from the times of the Civil War, so it's hard for me to relate to it. I only know a lot of mostly innocent and possibly related people got killed on both sides. I hate wars more than I hate flags. I suppose developers aren't happy about having their games pulled but they'll just have to bear with it. Most likely, they'll survive. They can make up their own flag to put in place of the Confederate flag.