I think you - and Iximaz - and Dawnfire - and Scapegrace - and whoever else - are misunderstanding here.
Neshomeh, July, and whoever else aren't saying 'this story/storyline is unsuited to the PPC', which seems to be the feel you're (all) getting. The analogy Nesh made to the earlier situation is instructive; it went in, mm, four or five stages.
1/ I wrote Reorg, Crashing Down, and Clbr__n. They were very popular.
2/ People (eg, Tawaki and Laburnum) decided that they were popular because they were darker/grittier/more interconnected/had deaths in. They started writing that sort of thing into their own stories - Tawaki did repeated arc plots, Laburnum... did Laburnum stuff.
3/ (Partly because of TVTropes) New people arriving thought that the Tawaki-Laburnum type of mission was how the PPC was all the time. They started trying to best it, with horribly-violent or convoluted prospective agents.
4/ The people who'd been here beforehand spent a couple of years going 'Erk?! That's not what we're about!'. It took a very long time to sort it out.
5ish/ 'Sorting it out' involved trying to increase the profile of more positive writing. I wrote Sandra and Freckles' first mission as an antidote to it; I also (perhaps ironically) killed off the DIO to get rid of the 'there are secret agents who kill others' darkness wandering around.
What various people are trying to say is that this storyline has put us into Stage 1: it's wildly-popular, consuming the Board, and making an impression. And that's fine; popular things are good! Neshomeh certainly wasn't saying 'Crashing Down should never have been written'!
Stage 1 is fine; it's just another way of saying 'sometimes stories are popular'. But... well, look at Matt Cipher's 'joke'. That's a classic Stage 2 response - 'you did it, so now I will too!'. And there's this three-way 'who can write the most missions' thing going on with Iximaz, Voyd, and SkarmorySilver; do you think it impossible that one of them would go 'hey, I could pull a LMM on my agents, too...'?
And then we'd have new people seeing just that sort of mission - the big, everybody-dies-this-changes-everything stories that we saw too many of last time. And we'd be sitting solidly in Stage 3.
What July and Nesh are trying to do (and, I guess, me, at this point) is shortcut to Stage 4: raise awareness of the fact that if people try and imitate this, things will go badly sideways. Hopefully, if that message goes across, we can skip Stages 2 and 3 entirely.
So, what should you do? What should everyone do? Not change. Iximaz has a moderately dark storyline going on right now, but apart from the agents involved in that, no-one else needs to. Keep letting Agent Des be cheerful, even though miserable things are happening elsewhere in HQ. If you're not involved in the LMM fallout, don't try to imitate it - don't give your own agents Dark Arcs because you think that's the way to go. Just... keep on being normal.
Short version: nobody's saying there's something wrong with the story. The concern is that other writers will try to imitate it and make it the new norm. Counter that by not doing so yourself.
hS