No it doesn't make them any less guilty (or at least debatable) but it does diminish their danger greatly, considering that cause of that danger was a mage and without him there would be no such situation.Too bad for them mages are still threat to the world.If i recall Arlik did pretty much good job or at least better than Thrask, so i would say somewhat acceptable job watching over the mages as far but could do much better.
Alrik was a templar extremists. It's men like him who are in positions of power and then abuse that power, that are to blame for every Circle Mage who snaps and for all the innocents they kill. It's these men who drive people like Anders over the edge. They alone are to blame - them and the Chantry, who has granted them that power and does nothing to stop them from abusing and mutilating those they were supposed to protect. If you want to see the world burn, then I suppose men like Alrik are your choice for ideal leader.
Red Lyrium exists even without Corypheus. Anyone could exploit that same weakness in hundred different ways. Templars are a mere tool of the Chantry, too bad they have proven themselves to be rather unreliable... a gun that will as easily turn against it's owner as it's enemies. That's lack of freewill to you. Maybe Chantry should consider tightening the leash... templars might be the next group they oppress and lock away in towers, who knows.