well i think the fact that giles went upstairs with a smile on his face with a bottle of wine showed he had intentions of forgiving and moving on. But unfortunately he was greeted by Jennys dead corpse rather than the horny Jenny he'd perhaps been hoping for...
However personally I think Giles and Joyce still would've hapened, the effects of the candy and the relationship between the two characters would be too great to stop it happening even if Jenny and Giles were still together.
I do feel that there relationship would've continued but for Giles haracter I think he needed to have the season four sense of no place, and not having the role he used to. I think if Jenny had been with him, it would've affected the characters transformation. Plus I couldnt really see Jenny as a long term scooby gang member, I think she would've left, perhaps following Angel to L.A.....who knows