Joyce knew that she was the reason Buffy left. She told her that if she walked out the door, she wasn't to come back, and Joyce feels incredibly guilty about that. So she needed to force the blame onto someone else, and Giles was the easiest person, because he knew about Buffy's life, but Joyce felt like Giles helped Buffy hide that part of her life from Joyce, even though Joyce had no real idea of what Buffy's like actually consisted of.
Also, if we think about it, although it was never mentioned at the time, Joyce had Buffy sectioned because Buffy told her vampires were real and that she was Chosen to fight them. She thought her daughter was crazy so she had her put into an institution. I imagine the guilt Joyce was feeling was unbareble and she needed someone else to blame besides herself. Willow, Xander and Cordelia were kids, Angel was in a hell dimension, so Giles was the only one she could blame.