Good question on Merle and Daryl's dad. I have no idea and guess I just assumed that he died.
As far as Beth goes, she's dead. Had she been alive, Dr. Edwards would have immediately started to give her medical care. Instead, Daryl carried her body out of the hospital to Maggie. While there was no funeral or memorial service, grieving was portrayed. Beth was referenced in the episode where Ty died when the group decided to take Noah home because it was what she wanted. She was also part of Ty's hallucinations. In the episode after Ty's death, a large part of the episode dealt with Maggie and Daryl's grief.
I think that a few may end up staying at Hilltop but Alexandria is the main residence for Rick's group.
About Negan, I know that he will likely be around for some time but agree that he should go. He was better in the last episode but I'm just not into him as a villain.