I usually get around the Grelod issue with a good character by having the character thinking it's all a misunderstanding with
Aventus, heading down to Riften to sort it out, being horrified by what they find there and either deciding the world would be a better place without Grelod or losing their temper, depending. I found the shackle room a long time ago and never doubted the rightness of killing Greold.
But yeah, getting back to what to do with all those quests in your journal: I just ignore them. I believe there are codes to get them out of your journal, but having them sit in there forever doesn't bother me. I mean, Skyrim forces so many quests on you, if you are a serious roleplayer you are going to HAVE to get used to lots of quests in your journal you will never complete, or else your character is going to be some overpowered king of everything jack of all trades with a morality yo-yo.