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.
