I think just having more mods is the answer. Correct me if I'm wrong on this, because I was totally ignorant of the problems Trans Era were experiencing, but I think the vast majority of moderators have solid ethical compasses, and the general moderating philosophy is great.
The problems I've personally noticed seem to be the result of an overworked, under-staffed team who often whip out the pruning shears (for thread closures and bans) more often than many Era users would like, in order to head off trouble that will cause them massive headaches before it truly starts. Due to the Trans Era threads, I'm now aware that there's an issue with under-modding as well. Again, I think the issue is the workload versus the number of staff members.
More staff means more eyes on each issue, which is another thing we absolutely need. I trust the team to augment itself with good people, and to keep itself in check, but it can't do that if it's spread too thin.
Everyone deserves some kind of considerate reply when they send mail to the Contact Us address, too. When you're banned, if you're not a Discord user, you're totally cut off. That Contact Us email is all you have.
Edited for greater specificity.