The truth is it's easy to maintain a big organization when everything is going great. People volunteer to help out, there's lot's of opportunities for profit, and recruits line up for a chance to join a winning team. But when things go wrong it can all go down the drain very quickly.
The simple fact is that EVE's current alliances have grown too large to be effectively managed by people playing a game in volunteer positions on their free time. Managing this stuff becomes like a full time job, and it's only a matter of time before people lose interest, real life interferes, or someone gets disgruntled and sabotages the organization from within. The game needs to be designed so that alliances are manageable and fun to help run and organize, not a second job.
I recently read that the CSM has impressed upon CCP the point that 0.0 has become "too small" because of the ease of moving large fleets, and that this capability has led to larger and larger alliances and a virtual stalemate in null-sec. CCP needs to aggressively redesign the sovereignty system (again) with the obvious goal of making New Eden feel larger and more dynamic. It needs to be a place where smaller alliances and corps war with their neighbors, not where everybody worries about the guy on the far side the the universe. Dominion should have been a golden opportunity to really redesign EVE's end game and make it something great, but instead CCP just tinkered a bit and the end result is a horrid mess.
What's happening to IT doesn't surprise me at all. It's exactly what's in store for every alliance in EVE. Eventually.