A lot of initial theory was written when the idea of complex markets and how they functioned was a relatively new idea. Compared to previous economic systems that were implemented, capitalism involved a lot less government involvement.

Crony Capitalism came about as an idea when established companies found it was cheaper to buy off the government for a better regulatory environment.

In theory you can have capitalism without crony capitalism, but it generally requires political power to be very diffuse and not concentrated in certain industries.