ouch, that hurts a bit. Freely downgrading regular runes was a thing for 13 years, ever since original Median XL 1.70 launched in late 2008. Pre-MXL it was required to have a certain number of Crafting Points equipped - they were found on gear and downgrading high runes required a lot of them.
I guess this will make jewelcrafting significantly harder because rn you can use almost any rune and downgrade it you find if you craft Lem-jewels for example. But this is alleviated by runewords being actual runewords instead of rune + jewels. Personally I hate rune + jewels because of inevitable stat bloat. You will get lots of trash affixes such as +1 light radius or +3 to life on such runewords.