The reason folks AFK waiting for NMs is kinda two-fold. The first is that, past a certain amount of people farming the monsters to pop an NM, more people don't help. When 130 people in a zone all crowd around the area for a single NM killing birds or whatever, the issue becomes more respawn time so past 30 or people there's really no POINT for people to help more. Obviously what they should do is go off and pop other things... except for issue #2: If you're not at the NM already or in a place with easy transportation (So, base camp), there's a very real chance that something may pop and you won't reach it in time.

If you want people not to sit around AFK while others work, you need to fix one of these. Fixing the first one isn't possibly unless you make it so kills aren't required at all... but that just makes EVERYONE AFK until the next pop, not just most people. #2 could be fixed by adding easier ways to get to a FATE location once it's popped (Say, a consumable like the Eurekan potion to return to base camp and a more robust aetheryte network) or giving some alert that an NM will pop soon or making it invulnerable for a couple minutes when popped.

Granted, there's also the option of just not making FATEs so OP. From a few things the devs said, it felt like they wanted people to primarily farm monsters and use NMs as a nice bonus... except the difference in xp and rewards is so vast that killing regular monsters is just not worth it, especially if you risk losing out on an NM. If you could farm monsters and reliably get crystals and xp, it wouldn't be quite as bad.