If there was serious metal to metal contact there, I imagine you would have heard it or seen a failure. Is it just a discoloration or is the metal of the crank case actually gouged or raised? It could just be a discoloration from oil slinging of the crank pin, heat or something like that. It's also possible that you had a small piece of debris in it at one time that is long gone.

Have you measured the clearance between the rod and crank case?

The magic question here is how does it run? If it were seriously rubbing, I doubt it would run well for long at the RPM's it sees.

Why did you pull it apart in the first place? Did there seem to be a problem with it? I've never had the back plate off of an engine unless the bearings were shot or it had some othr mechanical failure making it necessary.

I say that if it aint broke, don't fix it.