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…
Maybe that doesn't move the needle on whether they're a small non-profit or not for you, but it's different than a massive non-profit like, say, the Prevent Cancer Foundation, which also receives millions of dollars per year to facilitate their mission.