Don't decide whether to register things or not based on a value in the config file. Register everything, but disable the recipes and remove the items from the creative tab when needed.
You could override IForgeItem#getMaxDamage.
I've got some tutorial information as well as links to others here: http://jabelarminecraft.blogspot.com/p/minecraft-17x.html
Note that part of the confusion is that there are actually four fairly different situations related to capabilities:
Using existing capabilities (e.g. IItemHolder) in your custom classes
Using custom capabilities in your custom classes
Using existing capabilities on vanilla (or other mod's) classes
Using custom capabilities on vanilla (or other mod's) classes
I think people get confused because often a tutorial will be covering a case different than yours and so if you apply it you'll either be missing something needed or will duplicate something unnecessary.