I don't think most people think the TSAB is good exactly, just that most people look at what it does and conclude that, on an objective basis, most of its actions are fairly benign in nature and lead to overall good outcomes. No organization of its size is monolithic, and to act as though it is purely good or evil just because of actions by certain members is unreasonable. It's like looking at the fact that in America, it is an objective fact that some police officers abuse their authority, and concluding that law enforcement as a whole is evil and shouldn't be trusted.
As far as Graham's actions, your phrasing is inherently inflammatory, in that saying he was plotting to assassinate a 9 year old girl to make himself out as the good guy makes it sound as though Hayate's death was the goal of his actions, rather than a consequence. The objective fact that his plan would have resulted in her death doesn't change, but it would have been the same no matter who the Book chose as its new master, whether it was Hayate, or some hormonal teenager who took it as free license to treat the Wolkenritter as sex toys, or a sociopathic warlord who used them to kill hundreds of people to consolidate power. He chose a method that would assure one death to most likely prevent thousands or maybe millions. I recognize that you don't believe that the end justifies the means. However, if you were to put yourself in that mindset, can you honestly say that the decision he made was the wrong one? Just, try to think about it while only trying to get the best outcome.
His other actions, deceptions, sending his familiars to attack and interfere in the situation, I think everyone acknowledges as wrong, in and out of universe. I don't think there's really much debate on that. Your last two points though...what do you think the TSAB would have done, if they were told where the BoD was? You've already pointed out you don't have faith in the TSAB as the "good guys," so what do you think would have happened? Would anyone have been happier or better off for it? Waiting until the Book was complete to freeze it, I may not be correct, but I think I remember it being specifically noted that it was actually necessary for the Book to have been completed in order for it to be frozen permanently (as in, doing it earlier would let it come back again later).
And his punishment...I'm fairly certain the home he lived in was his personal property, rather than anything given to him. His personal assistants were his familiars, meaning they were dependent on his magical power to live. Separating them would have been effectively sentencing them to death for his actions. In the end, I think it just came down to whether it was worth the effort to do more to punish him. No one was permanently harmed, the Defense Program will never be a problem again, and his primary goal was to stop the Book from ever being a problem again. Given that he'd been involved with the TSAB for 50 odd years, it was probably an "In light of your many years of dedicated service" answer.
@Van
Precia's illegal actions were completely different. Graham wanted to permanently stop a dangerous Lost Logia from rampaging, even though it meant committing crimes. Precia committed a bunch of crimes personally and by proxy to get a set of Lost Logia that she would use to tear open a hole in dimensions because she thought it would get her to Al-Hazard, where she would be able to bring her dead daughter back to life. From the TSAB perspective, you have one guy who broke rules to do what was essentially his job taken to an extreme versus a woman who went crazy after her daughter died and wound up dragging a bunch of people into her quest to go to Super Magic World and resurrect her daughter. They just...don't really compare.
And Hayate...we really have no idea what would have happened to them if they didn't take responsibility for their actions, because they did. It wasn't like Hayate was forced into it, because she specifically chose to join the TSAB to take responsibility for what the Wolks did because she sees them as her children. Them being "hunted"...Jail Scaglietti only gets put in prison for all the stuff he did. Granted that they're using his knowledge, but given that and that Midchildan magic is set to stun at base, I doubt they even have the death penalty. At worst, they probably would have gotten some prison time for their crimes if they refused their "community service," and likely not much, considering Fate went free because she was just trying to help her mother.
"Ruining little girl's life"...Gil did that, and Precia didn't...did we see the same series? Precia whips Fate for not collecting enough Jewel Seeds, tells her how she's just a worthless doll that she never cared about, and the only reason Fate is able to get over it as quickly as she does is because of the Book of Darkness illusion thing she gets put into. Gil supported Hayate after her parents died, and tried to make sure she would suffer as little as possible before being frozen with the Book of Darkness. If he were so callous, why bother supporting her at all? All he needs to do to stop the Book is to keep track of her and make sure she doesn't die, but he doesn't just stop there. Sure, it's because he feels guilty about what he has planed for her, but that in itself proves that he sees her as a person and not just a tool or a sacrifice. Really, Hayate wouldn't have grown to be the person she was without Graham's financial support.