Right, Jowan's story really doesn't matter unless they decide to write up some reason to include him further. The only way he would continue to exist as an interesting character would be if you freed him and told him to run in Redcliffe and then let him live when you ran into him again. Other than that, either you kill him, Eamon kills him, or he goes to the Circle where he is likely made Tranquil. So it is unlikely he would ever be seen again except in flavor cameo, like running into Fist or Helena Blake in ME2.
He could end up being one of those swapped characters like a certain handful of would be wardens in Inquisition or like Wrex in Mass Effect.
They havent needed to worry about that since the game was feature complete. Their current focus is on DA:I choices
Like I said it's obvious the focus is on Inquisition now, so only the choices effecting that game should be a priority, but it would be interesting to know if down the line say in a DLC or new Dragon Age game the Keep would update some of the other choices to get some of that nostalgia of longtime players or players who just like to fiddle with the Keep.
Especially with the possibility of something dealing with The Calling I could easily see some other characters from Awakening return, but considering their endings are non-existent in the Keep that would cause a bit of a problem unless they chose to ignore them completely or have them added.
I'm not angry and Bioware for not including everything it's a tall task, but the greedy fanboy in me wants everything to be included just for that off chance Bioware is like "Hey we should do something with this choice, good thing we have it in the Keep already." 