You're finding it "hard to side" with a literal nonprofit charity getting bullied ruthlessly because something something SaaS not self-managed? My God, dude.

This isn't a charity focused on aiding the homeless or something like that. This is a charity focused on teaching programming. When there's perfectly good open source alternatives to slack it IS their fault since they should know better. If not for being immune to such problems then atleast for saving money since IMO a non profit should be as lean as possible. A for profit company can justify using a SaaS in a cost / benefit calculation, having to face competition so they need to move very fast etc. This isn't the case for a non profit.

I have always found the argument of "They deserve this because they should know better" to be a very bizarre way of thinking.

It implies there is only one correct way to think or to prioritize or to approach a problem. It also (pointlessly) tries to shame someone for something that has already happened and cannot be reversed.

I would find it hard to side with Jesus Christ himself if he decided to start teaching via Discord server.

I wouldn't mind if it comes with fish and wine. On the other hand, I believe Discord will be the next bomb for too many communities/groups out there. Or maybe after they get acquired first, either by a PE or a PE-esque corp (e.g. Salesforce, Oracle).

What does a dude from centuries ago have to do with all this?

It's reductio ad absurdum with a twist, and that dude is the typical shoe-in for hyperbolic examples that need a moral paragon.

I feel like communities have very good reasons to at least consider the option where the most users (since this nonprofit focuses on teens) are already using

The number two focus of a charity should be good financial management. First being the charity's mission. I would not support even a large charity to pay $200k/yr for a chat server.