My suggestion is when you unlock a skill, you have all skill runes available. When you select a skill rune, you are stuck with that skill rune for your level. When you level up, you may select a new skill rune or keep the one you have.
It does pose a problem at later levels when it might take 12+ hours to level and you selected a skill rune that you find to be ineffective at the time, but im completely open to new ideas about how this system could change. Like perhaps the Nephlam Alter makes a return but instead of changing skills at it, you can change skill runes. Skill runes are still all available when you unlock a skill and a permanent until you reach an alter.
Edit: spelling errors