Just for your (and others') reference, the magic item in question is a non-standard LCO item, so this isn't exactly a common scenario for PCs.
Anywho, if you are immune to a carrier, you are immune to the entire effect. That said, you are immune to Disease while bearing the item, so if a creature is swinging for the Disease carrier, you are immune to not only the Disease effect, but the damage as well. You will call "No Effect" to it and take no effect.
~ Alexander
SoMN Rules Marshal, and the guy that put out said LCO bearer-is-immune-to-disease item as loot a few events ago