Before you follow through with this new rune method, know this.
There are three kinds of players that I will differentiate by "upper class," "middle class," and "lower class."
Upper: Have every (or close to every) champion, rune, and runepage available. They typically can afford every new champion release due to having plenty of IP in their wallet.
Middle: Probably where most of the players live. Have just enough runes and champions to go off of, but are far from owning everything. They typically don't have much IP for long.
Lower: Just got into the game (or haven't played for too long). Have a few champions and probably no runes. They probably spend IP as soon as they get it.
If you implement this system with such low refund values, you're screwing over a ton of people.