Is there a system biology approach to compare pathways or famillies of proteins from an evolutionary point of view for the same organism?
I am not sure that I completely understand, it would be a little easier if you described the problem you are trying to solve or what the motivation is.

However, I think that some of what you want to do can be accomplished by inferring gene/protein trees for each gene/protein of interest across different species (including paralogs, maybe?). This will allow you to see discordance or correlation of evolutionary rates of different genes/proteins across species. 

THis kind of analysis is built into HyPhy, though I have never used it. There are also somewhat less involved methods for measuring distances between trees.

You might also be interested in protein co-evolution methods, depending on the question at hand.

Your mentioning systems biology methods suggests that you have something rather different in mind, as none of these things I suggest are really systems biology IMO, but I'm not sure what it would be. Possibly you are interested in integrating e.g. protein-protein interaction or metabolic network information as well, but that would probably involve something more homebrewed that might integrate some of these things.

Hope that helps.