WOW

Ok first off you can change rune x in to rune y its easy

If say you have a level 10 bane and want it to be a vengeance now
You get a level 1 vengeance and merge it with a level 10 bane and its now a level 10 vengeance.

Now you cant take a level 5 Adept and turn it into a level 6 wall. But you can turn it into a level 5 resistance or nimbleness if you have a level 1 of those.

Why you would actually want to change the runes you have into different runes is beyond me. Once I have a yellow rune, I wold not give it up unless I have 5 of them.
All runes are important at some point in the game with any formation. Taking a level 9 bane and breaking it down into generic runes to reuse the experience to level something else up seems odd to me, unless it were to put it into a vengeance which you can already do.

I think you are over thinking some parts of this and under valuing and under thinking other parts of the game.

Perhaps if you could give us a clear exact example of what you would like to do using the heroes and runes ?