And yes, he has no pvp gear at all and I have a couple pieces.
How much, in percent on the base item value, is the penalty ?
While I do agree that a lot of pvp gear is not as good as lower rated non pvp gear for pve, there are for every class certain slots where the pvp item is clearly the best choice. I can see that the identification of these items may be difficult for Heroes, but as long no one can do it, we'll never have any tool that clearly tells us what toon has the better gear.
To make the item values you use to calculate your hero score more transparent I would suggest you display the item value of items with resilence as a modified value, not the original value. So everyone can see right away what value the item really has. This would avoid confusion and make heroes a even more valuable tool for players to determine how good there gear is for PvE.