On the topic of Bill, I do think maybe Bill, being the oldest brother and probably having a protective instinct, might have noticed that Harry/Ron had disappeared; however, we have to remember that there are at least 70 Gryffindors at Hogwarts. Percy and presumably 5 other Prefects had quite a task in evacuating all of them back to Gryffindor Tower safely, so in that sea of 70+, I don't blame them for not noticing that three first-years were missing.
And yes, throughout Order of the Phoenix/Half-Blood Prince, Percy's behavior was absolutely difficult for me to sit through. I really felt for Molly. I remember feeling outraged like Arthur. I remember glaring at the pages just like Ron as he read that letter and then tore it up. Like Pam/wishes said, it all made for a very extreme rebellious stage in Percy's life, but it made the redemption all the more... real, I would say. Because even for me, when we saw Percy show up at the Battle of Hogwarts. I remember reading it and being like, okay... Is he for real this time? Is he finally on our side? Do I even want him back on our side after all he did against us? But in the end, Percy's family, and he saw the error of his ways. I really liked that resolution. ^_^