While it appears "logical" that whatever the enemy says is not to be believed, you, as a leader, are going to face internal struggle for power (multiple), discontent about how a fleet commander conducted a fight, burnout from the struggle (in a campaign, if you do not keep it up for a long time, all you did so far becomes useless. And if you do, success is still not guaranteed), conflicts between the PvPers crying for more numbers and calling the industrialists and logistics to fight, and the industrialists and logistics that are not interested in PvP. Or the industrialists lamenting lack of local defense/logistics because the fighters are away from home.
I'm not seeing how scale affects any of this stuff, which appears to be the only relevant section. More of it to handle, more people to handle it. Create a culture, don't dictate behaviour. As the organisation grows larger, that becomes even more relevant.
It still sounds like leadership issues. I never had a problem with enemy propaganda (particularly in the vein of 'they're not really your friends!'), and it wasn't for lack of trying on their behalf. You would have to find some very gullible people to buy into that kind of thing. On the other hand, we never lost so I'm not really in a position to understand first hand the kind of pressures that can put on an organisation.
Oh, btw, not that it seems particularly relevant, but I did mean 800 in the alliance, not the server. Still very small scale compared to eve from what I hear.