More than a "punishment" is a tax for be an hybrid class. Also, consider that as a shaman resto/elem I swicth very often.
When you are at levl 102 you gain the quest for the second and 3rd Artifact and you gain Artifact Point for the artifact equipped. So, as a healer*, even if is doable, I preferd go to dps during exp/quests, but spending my AP on Resto Artifact.
Also, runes (as all the rewards) that you can recive from quests, change based on your spec. So if you wanna the resto Runes insteed of elemental ones, you must change spec before finish a quest and choose your reward.
That means not only you change spec from dps to healer when you queue to a dungeon but event during the exp phase if you wanna spend AP/runes on an artifact different from the equipped one. Runes are used not only for a +1 skill point but for increasing the item level of the Artifact.
That depend how you wanna play, is not a big concern for many players, but is it for players like me that use 2 specs.
*Exping in a healers spec is doable, just as I say, but is slow and its boring like as hell... and dont make any sense kills mob in a spec used for heal players, when I have a spec born for that job.