The Upgrade Menu in teh demo scene is just an example on how a Upgrade system could be built with UIS.
It was not designed to be very flexible. You can learn about other ways UIS can be used to upgrade items here:
There are many ways to upgrade an item: Parent/Child Item Definitions This is the recommended approach if you have a simple upgrading system where upgradable . . .
opsive.com
So what you are trying to do will require some custom code. The code is fully commented so you should be able to follow trhough even if you are not an expericenced programmer.
The best way to start is copy paste all the code related to the UpgradeMenu. (Which if I remember correctly is the UpgradeMenu and UpgradePanel)
Then in the function where you equip the Runes you'll want to add a check to prevent adding the same type of Rune.
A simple loop over the array of currently equipped runes with a check to see if it uses the same itemDefinition as the item you are trying to equip should do the trick.