Except that, no, those really aren't answers that resolve the fundamental issues here. The question that's been raised is "Given that the TSAB is an organization that would destroy the Scrya with overwhelming force either because they were strong enough to be a potential threat to it or as a scapegoat to make people believe in the TSAB, why would they not respond similarly to Precia and the Wolkenritter?" Your answer was that the TSAB wanted to use them, Precia for her expertise and the Wolkenritter for their strength, and that it could manage them (given that they would definitely not want to work with the TSAB) through brainwashing and manipulating Hayate, respectively. Except that neither method actually deals with the biggest problems.
Precia spent years after leaving focused purely on Al-Hazard and bringing back Alicia, so her "expertise" is very plausibly out of date in the first place. Secondly, brainwashed people typically don't have all of their mental faculties available, so they would be dealing with an emotionally unstable mage whose knowledge may be old, who probably doesn't have all of her impressive brain power available, who has some level of terminal condition, and who would do something horrible in revenge if she ever happened to come back to herself, either by going on a magic rampage or sabotaging whatever she was doing. The alternative answer would be to use a less capable person who is in fine health, who actually willingly works for the TSAB, while nuking Precia and either explaining it away as her conspiring to destroy Midchilda or some other convenient lie, similar to what it did to the Scrya.
As for the Wolkenritter, yes, they're quite capable in combat. Except that they come as a package with the Book of Darkness, aka "That thing that destroys planets." You said the TSAB could control them by manipulating Hayate, except that, until the end of A's, that still leaves the Book as a problem. Nobody knew about Reinforce, the Defense Program, any of that, until Hayate took control at the end of A's. As far as everyone knew, that was just what the Book was designed to do. Even if it's a setting with multiple planets, destroying one isn't a choice they would just make. It's like having a team of secret agents that come with a nuclear time bomb: sure, you've got a group of cool spies to do cool spy stuff, but if you keep them around long enough, a nuke is going to explode in your face. And once the Defense Program is destroyed and that problem is resolved, they're already working with the TSAB more or less willingly. So the options are to bring this group of good but not outstanding mages to work for the TSAB while trying to figure out some way to deal with the inevitable world destroying monster, or nuke them all including the Book while pointing at the times on the record that the Book and the Wolkenritter have destroyed stuff as an explanation. If A's has already happened, then it's a question of "treat them like normal employees" or "let's blackmail them with their master so they'll resent us and be looking for any way to get out from our control."
I'm sorry, there's just no conceivable way to convince me that an organization that would make a preemptive strike against one group that represented an unclear threat would be so alarmingly stupid as to try to control other parties that represent clear and obvious threats, including, and I can't emphasize this enough, coming as a package with a planet-destroying magic device. At least not an organization that would be able to establish itself the way the TSAB did.
And for Yuuno...so it's Yuuno with his canonical feelings on the issue, just apparently with enough of a buff to actually be able to handle the rampaging Jewel Seeds on his own. Because that's exactly what he wanted. He tried to get Nanoha to give back Raising Heart, go home, and be normal, but she refused.