In the episode "Papa Don't Leech" (S19E16) unconscious Homer dreams of suffocating his father (however, I personally think that some of the modern episodes shouldn't be considered as canon). Does this scene confirm that Homer wishes for his father to die, or even would like to murder him with his own hands?
There's a few facets to this question.
Firstly, don't read too much into a throwaway gag. Comedy shows like the Simpsons put gags before worldbuilding and are thus liable to misrepresent the in-universe truth in favor of something that's funny.
Secondly, Homer chokes Bart regularly (at least, he used to). There is no indication that he's trying to kill him either. Strangling is fairly common in The Simpsons, and it does not signal hate or intent to kill.
Thirdly, Abe was not the best father to Homer. Especially in flashbacks, Homer is often ignored or insulted by Abe. While this is more or less intended as a "sign of the ages" rather than pointing out Abe's behavior as atypical, the fact remains that Abe has left Homer with some resentments.
As Homer is prone to strangling those who frustrate him, it makes sense that his dream has him strangling his father as a way to vent his frustration.