I think Giles did eventually forgive Angel but I don't think he ever fully trusted him again. Giles was aware of what a soul did for Angel, so I'm sure he was able understand that it wasn't Angel who killed Jenny; however Giles always remained aware of what the cost of Angel losing his soul could be.
This is illustrated in Season 5 of Angel's own series, when he refused to help Fred because of Angel's association with Wolfram & Hart.