That said... simply cost prohibitive based on the spherical graph would work great as well and is honestly my preferred choice here.
Limiting players to one tree, any way you go about it, is limiting to gameplay and strategy options. Right now, if I want a "Chaotic Neutral" style civ, I can make that. If I want to pick and choose - both for individual worlds and overall ideology - what best suits my strategy, I can do that. The big thing to me is the ability to shape a civilization to create a unique personality. Diplomatic with an appetite for war. (pragmatic, malevolent) Militant isolationists who take care of their own, but are aggressive to outsiders. (benevolent/malevolent/vigilant) Dedicated Pacifists. (benevolent/pragmatic) Masters of manipulation (affinity, prominence, traders, negotiators, awe, motivation) Crusaders, Paranoid, Hyper-capitalists, amoral, passive, I can think of so many ways to craft a civilization.
Otherwise, it's simply Good/Neutral/Evil and that is boring. A system which pushes or forces us in one direction is a system to which I am vehemently opposed. It makes for linear strategies and predictable opponents. There's no personality. I would welcome more options, rather than fewer - more flexibility, not less.
The most effective way of dealing with any problems is to:
A)Let AI use ideology strategically (or in interesting, goal-oriented ways), and
B)Give the galaxy creation option to make ideology cost more (or less) overall. This way, if we create a galaxy with a whole bunch of planets, we can raise the cost to make it take longer to earn traits.