I want to get the meaning of the following sentence:
if a program is crystallized thought, ...
Does it mean a well-planned program or well-made one?
Neither. It is a metaphor meant to describe programs in general, not describing or referring to a particular program, or even a particular kind of program.
The metaphor imagines "thought" as being like something dissolved in a fluid, that gradually crystallises out into a solid, structured mass, and the program as the resulting mass.