I probably would have attacked the passive problem a bit differently. Making them die was a "hard control". I typically use "soft controls". In this case: make it so that passive flowers are progressively self-defeating.
One way to do this might be for passive flowers to emit a sort of "flux" that makes flowers (as a whole) less productive. The more passives you have, the less productive any nearby (?) flowers become. With, say, 10 or so passives, you wouldn't notice a penalty, but once you get up to 50, maybe your orechids are suddenly useless, your endoflames are weak, and hopperhocks take way too long to grab stuff.
Actually, that's exactly what I would've done to. Set a limit, X, flowers of a certain type. More than that in the chunk, or adjacent chunks, and you see a reduction in output, with a sliding scale down to y number of flowers where you just hit zero.
And really, I think the bigger problem here isn't necessarily grind so much as changing a player's expectations.
With Botania, it was seen as largely a 'casual' mod. You planted flowers, they produced mana. The change to cause passive decay caused so much flack because the expectation that the players had come to rely upon, that flowers, once created, didn't just vanish, was reversed. And, to quote Heath, 'well then, everyone looses their minds!'.
It's not just adding additional grind (and by grind, I mean adding in content that is not engaging for the sole purpose of extending the number of hours it takes to play through content), it's changing a fundamental concept of the mod's mechanics. You had a heel-face-turn and suddenly got hit in the face with 'all my flowers died!'. Naturally, there's a bit of negative feedback. Enough so that it caused someone to fork Botania just to remove that. Which, according to Curseforge, at one point actually had more downloads than Botania itself did.
And, in fact, let's explore this a bit more, because there's another concept here. I don't know who here is familiar with 'the power of the default', but it's the core power behind Microsoft's business model. Basically, the assumption is that 90% of your users will never bother changing settings away from the default settings. Think about that a moment. Nine out of ten users never bother touching their config file, especially not if they are playing a pre-created pack from one of the launchers.
When Vaskii included passive decay, it started off as an option. Then it started 'on' as the default. Which apparently enough people turned off to cause Vaskii to decide to remove that option. Rewind that, play that again. Enough players and server admins bucked the power of the default and turned decay back off. This was an active decision on the part of these people, you had to go in and change your config file. Sure, it's not a lot of effort, but it is an effort that, typically, you don't see much of. So that enough players were going in and changing the defaults (and remember, server admins had to also make this change deliberately and consciously for it to work on that server, so we can't put all the blame on the end-users) is pretty staggering.
To me, personally, it would've been a clear warning signal that maybe I need to implement some other fix to the problem (passive flower spam lagging out servers). And I'd like to think I'd have implemented the feature Pyure and I have endorsed.
I have absolutely nothing against challenging mods. I think they are great for those who like them. The problem is when your mod, however inadvertently, catered to more casual players, and suddenly a mechanic changes to make it less casual and more hardcore, you're going to see a dissonance, and quite a lot of drama.
There are mods like GregTech, and there are players who like playing it. And that's great. And you know, going in, from the moment you install GT, that this isn't going to be a mod that hands you everything on a silver platter. Your expectation, as a player, is that this is a mod which sets a high bar on skill level with the mechanics and concepts introduced in the mod. That is good game design.
There are more casual mods like... let's say MFR. You understand that this isn't a mod which is going to challenge you, it is there mostly so you don't have to keep farming renewable resources so you can go do more enjoyable things. This is also good game design.
You would no more expect machine explosions in MFR than you would a single-block early-game solution from GregTech. Heck, remember the furor around the April Fool's Joke that Direwolf20 did earlier this year with BC and IC2 switching some fundamental concepts?
This is what things like the ignoble bee nerf or the passive decay nerf is doing. It is changing fundamental concepts about the mod as we understand them. And change is something which human nature has a great deal of difficulty dealing with.