There must be some kind of mistake, or some details getting left out here. Usually Salesforce (the parent company) is pretty nice about offering discounts to nonprofits. If they are losing the discount, could it be that maybe it's because the clients they serve (i.e. the people receiving help/services at their nonprofit) are treated as "active members" of their Slack instance? I'm not too familiar with Slack pricing…
This pricing model makes no sense for a non-profit that is trying to teach coding to teenagers worldwide. They will have a lot of users (remember) who might only send one or two messages once in a while. having to pay $7.25, for some who just asked a single question, is essentially extortion for a non profit like that who's primary purpose involves reaching out to as many people a possible.
> then I think that means they have over 2,000 active members in their Slack which does not sound like a "small nonprofit" to me.
those are not employees, but most likely the people they are trying to help.