Sorry, if this is a naive question, but I could not find the justification in any of the major text books like Bondy-Murty, Diestel or West. Perfect graphs have many beautiful properties, but what is the single reason they are called perfect? Or is it just a aesthetic preference by Berge?
perfect graphs were first motivated by information transmission theory originating with Shannon ie Shannon Capacity of graphs. they are called "perfect" by Berge because they can be used to model a noiseless or "perfect" information channel wrt transposition errors in transmission called "confounding". from intro in  which also has a very detailed history in the 1st chapter cowritten by Berge.
When Claude Berge defined perfect graphs in 1961, he was motivated by a very practical problem: how do we maximize the rate at which information is sent through a (noisy) transmission channel while avoiding the introduction of errors because of the physical imperfections of the system?
 C. Berge, The history of the perfect graphs, Southeast Asian Bull. Math.
20, No.1 (1996) 5-10.
 C. Berge, Motivations and history of some of my conjectures, Discrete Mathematics 165-166 (1997) 61-70.
 Perfect Graphs by Jorge L. Ramírez-Alfonsín (Editor), Bruce A. Reed (Editor), J.L.R. Alfonsin (Author). Wiley. Ch1, Origins and Genesis by Berge & Ramírez-Alfonsín