As many have pointed out Anders deserting is obvious, and he goes into hiding because of it. Now you complain about the narrative forcing you to do the joining, just as the narrative forces Anders to live until the end of DA:2.
Multiple people had right to execute him, yet chose not too. The wardens Anders can run in to are Stroud and Nathaniel, Stroud appears to owe him a favour so chooses not to execute him and Nathaniel and himself were comrades, so again he dodges the bullet there. It doesn't mean no Warden will try to kill him, they already tried before he went into hiding, the order attempted to have him killed after his becoming an abomination came to light. He killed Templars and Wardens working together then fled from both.
So yes he is being hunted, he may not be public enemy #1 so not every resource of the Wardens are used to hunt him, instead, just a standing order, if you find Anders, kill him.
Hell Hawke had every right himself to kill Anders as an abomination but the narrative doesn't allow us, we are bound within it, if you do not wish to be bound to their narrative your option is either do not play or head cannon it away. It won't change the official narrative though.
Jory also tried to desert during the joining, how did that end up for him? Oh right, Duncan killed him. Just as he would have if they allowed the HoF to try to desert and ignore the right of conscription. It would have been humorous had they allowed us to try though.
A few people have illustrated why Alistair hasn't been actively hunted after the 5th Blight and it could also simply be he was pardoned for his assistance in ending the Blight, but if he is your Warden ally in DA:I he is actively being hunted for going against the order. Just like Stroud or Loghain if they are your ally instead. They are considered higher priority and so actual resources are used in their manhunt.
There are many examples throughout history of people getting battlefield promotions, temporary commissions and brevet ranks, the same happened to the HoF during the 5th blight, they would be considered acting Warden Commander during the blight, the needs of the moment making it impossible to have it officially ratified, when it is possible to restore a command structure those in charge can choose to make that change permanent and official or declare it void. In this case they chose to make it official and give the HoF the title if they survived.
Riordan could of usurped command if he chose, but is probably wise enough that it would of caused more problems than it would have solved, so instead slipped into an advisory role for the HoF.
Now to use Komandor's own analogy against him, does a police officer have to get the okay, permission and order from the police commissioner to arrest someone for shop lifting, or attempting to stop a murder? No, they have standing mandates, just as Wardens do. Orders coming down from above are usually in regards to deployment, not, 'oh see that guy stealing that car, go arrest him'.
So the order does not need to hold your hand and coddle you at all times, treating you like a special snowflake for you to be part of it, that is just ridiculous and not possible in this time setting. It could take months to get orders back and forth from the Anderfels to Fereldan, are the Wardens expected to just sit on their hands until they get an order saying, stop the blight! No, people in any job are expected to be be able to perform their function without constant supervision, and the Grey Warden Order is more autonomous than most.