If you do not like the rune fusion function, dont use it. as simple as that i suppose.
Does it upset the game balance? if we focus on 3 and 4 star runes, then obviously the intent is for end game players to be OCD and squeeze and maximize their units stats
For 1, 2 runes merging, it surely help the new players or those who have poor luck. Since now u can get 1 3 star rune of ur choice more easily everytime u farm a heroic or exchange for rune tickets from bazzar( 2 stars).
Like many others. i do find 3 star and above runes promotion expensive, but will it still be expensive to me 3 to 6 months later as I continue playing? Or by then will I actually find such initiatives useful?

Devs alr help reduce reliance on RNG and make life easier for us, nothing much to complain about. Because whether you choose to do anything or nothing, it doesnt make you worse off.
And no, it doesnt make whales OP or make a bigger gap. Those willing to fuse 4 stars runes alr paid the price and are willing to make the sacrifice. Even without such a function, players that dont wish to make similar sacrifices be it time or money will never catch up. Thats just how it is. Gap is already and will always be there. And its an acceptable level.
So yea, every function good or bad depends on your perspective.