Ideology is an interesting problem. Arguably your actions should dictate what Ideology you are unlocking (somewhat, as it does now), but it gets quite odd, quite quickly, and your ability to cherry pick is too strong in my opinion. If I could, I would have modded the system as such:
Ability Chain A )
Choice 1/2/3 (Corresponding to ideology)
Ability Chain B )
When you have X many ideology points in Benevolent, you can choose to unlock Choice 1 in either Chain A or B. Doing so though, is mutually exclusive with Choices 2 and 3 of that chain.
So for example:
Ability A) Colonial Policies
Choice 1) Freedom to Explore! Colonists are happier (being purely volunteers), but grow slower.
Choice 2) Incentive based Colonialism! Colonies grow faster, but have a small fiscal penalty when not pop-capped.
Choice 3) Forced Migrations! Colonies grow much faster, but happiness takes a big hit until pop-capped.
I'm sure you can guess how these are laid out. The point is, you can be "Malevolent" regarding your Colonial Policies, but perhaps you choose "Benevolent in another category. You cannot be Malevolent AND Benevolent in your Colonial Policies. You have to make a choice and sacrifice some opportunity. This also has the bonus of allowing the B,P,M mixture of ideologies to produce combinations that might actually seem realistic.
Communism might be a "Malevolent" force in population matters, but fairly Benevolent in economic matters, and down the middle in terms of military aggression... the Soviet Union having forced many populations to relocate, but in theory having the people's interests at heart, and again, in theory, being a "peace-loving" nation.
The Capitalists of the era wouldn't have been much different, perhaps a bit benevolent in some areas, pragmatic in others, and such.
With this system the "Ideology" of the player is rarely ALL B-P-M, (you'd have to be purposely choosing one line only) its the unique combinations of their actual policies. Those combinations are INFORMED but not entirely DICTATED by your choices in colonial events and such.