Jowan was never much of a strategist, but I usually helped him because I had no real reason not to. Unfortunately, when you know for certain that Duncan's going to recruit you no matter what actions you take, it sort of takes away from any feeling of consequence for breaking the law and making moral decisions that have the same net result at the end of the origin. People will react a little differently later, but I can't say those reactions had much impact. So I helped the fool, if for no other reason than because I don't like Templars controlling mages. Also, why make Jowan tranquil, anyway? He's so monumentally weak that he can't even become a full-fledged mage. I can't imagine a whole lot of demons are lining up to take him as their host. I don't think he even knows that blood magic can be used to hurt people. At the end of the origin, all he did was give himself a crippling injury in order to knock everyone down for a second and run away. He could have killed them all, and instead he used their gigantic armour against them and made good his poorly thought out escape. Maybe that's why Irving didn't bother using his own vastly superior power to stop him sooner. He knew Jowan wasn't a danger.
As for the blood magic thing, I'd say it's just as dangerous or harmless as the mage who uses it. People don't freak the hell out over mages controlling water, because that doesn't really come from in our bodies and isn't psychologically linked to life, but once a mage figures out that they can move blood back and forth in a similar manner, they're branded evil because blood is scary, and people don't realise it can be of much greater use to healers on the battlefield than anyone else. I love how ignorant and superstitious the vast majority of Thedas' citizens seem to be. Then again, blood magic is also supposed to allow users to take away their victim's free will, so there's that. Again, that comes down to how dangerous the mage is.
From the Templars' point of view, I guess you can see their paranoia of blood magic, since knowledge on how to use it comes from demons. That said, if they actually stopped killing blood mages, then only one needs to deal with demons, and they can then teach others how it works. Dragging things back to Jowan, I feel like that alone is enough reason to let him go later. He's not a danger to anyone until forced into it, on account of him being kind of a coward. If you let someone like Jowan, with minimal magical power but plenty of knowledge and good intention roam around, he'll probably start teaching stray mages how blood magic can be used in good ways. They'll all then be killed because red liquid is scary and maybe something about demons.
I also read once that Jowan was originally meant to be a potential party member, which I actually would have liked to see. He would have brought a different kind of attitude to an otherwise largely positive thinking team. It would have been like keeping Jory alive, or something. He'd be the guy at the back of the groups muttering "I really think this is a bad idea" every time someone starts outlining a big, deadly plan. I can understand why they cut him, but I still think he would have made an interesting companion. A melancholic mage trying to find his place in the world, a social misfit with additional stigma attached to him because of his powers, and then he's a self-centered pacifist until backed into a corner and survival depends on action. He even seems kind of impressionable and naive, in his own way. A sort of diverse character ripe for the molding into either a confident and goodhearted mage that could act as a heroic figurehead for magical reform, or fuel his resentment and turn him into a cold-hearted master of the dark arts through his companion quests and stuff, kind of like when hardening Leliana or Alistair. Like a gloomy, antiheroic Merrill type character.