You can't make a rune in Haven. You need a blank runestone on top of those corpse hearts and you can only buy them in skyhold.
Or is there a seller somewhere earlier that I don't know about?
Have you tried Val Rioyoux? I swear there was a shop that early on that sells them.
After my last post I remembered that you can't even craft your own runes until you reach Skyhold, so I guess this discussion is a bit redundant. 
Actually, you can craft runes prior to the Battle of Haven! After completing "In Hushed Whispers" or "Champions of the Just" (i.e. choosing the mages or templars), a new shop opens up in Val Royeaux with a dwarf proprietor named Havel. He sells the blank runestones. Prior to the Battle of Haven, you should be able to locate the base Fire, Frost, Lightning, and Cleansing rune schematics. Locating crafting materials for the frost and fire runes is easy, open up the appropriate doors at the forbidden oasis and farm fire and frost essence. I'm not sure where lightning essence comes from.
For me, half the fun of DAI is preparing for the various big battles by crafting the best armor and equipment you can find. Prior to the Battle of Haven, two things which you can do to give your stuff an added punch is to locate Tier 2 crafting materials, particularly metals, and craft some basic runes.