The only thing you can't do while raging is cast or concentrate on spells
The Barbarian's Rage feature states:
[...] If you are able to cast spells, you can’t cast them or concentrate on them while raging. [...]
This is the only sort of restriction the feature applies on anything magical. The runes do not involve casting spells, if they did, they would explicitly state as much like the Way of Four Elements Monk does with its Fist of Four Thunders feature (and many others):
[...] Some elemental disciplines allow you to cast spells. [...]
[...] You can spend 2 ki points to cast thunderwave. [...]
This feature explicitly states that you cast a spell, and since the Rune Knight's Runes do not include a similar wording, they are not considered to be casting a spell and thus a Barbarian can use them while raging. There is a somewhat similar case with an Artificer's Spell-Storing Item where since it does not explicitly state that you are casting the spell, you are not actually casting it.