Rune refunds are fine being low, because remember that you are also unlocking all the other runes.

It's highly unlikely that you own ALL the runes, and even if you do, you've played the game well over 4000 hours, and likely own all the champions, so what he hell are you going to use the blue essence for anyway? You can only spend it on champions. And if you own all the runes, then you're either sitting on a fat stack of IP right now or you just finished buying them this year, meaning a full refund. Also, all those "shit" runes that everybody told you not to buy are now yours so a lot more testing and potential diversity in the future.

Finally, they're adding a bunch more runes that that extremely powerful and you can't possibly have owned before. For free. Imagine the worth of all those runes as well. Also, with the amount of ways Riot has been adding to get free shit (loot and honor), they can have a bit of wiggle room.