They kind of did establish a rule though, with the intro that played in every episode. Aku says "and undo the future that is Aku!", which greatly implied that Aku knew that if Jack returned to the past and slew him then, it would destroy both the future and its Aku. The problem we face with the ending is that there's no hint given to whether Jack is aware of this and how it would make him feel. One would imagine he'd feel some guilt about basically wiping out millions of trillions of lives (probably more if we count every all the lives from when Aku's empire began to its final point in the future), but instead he just looks sad about losing his love.
As for whether Genndy had something in mind, I think he kind of did. When the Duck Dodgers parody episode aired, Genndy (playing a Flintstones-like version of himself, but with future parts) basically boiled the narrative down to Jack learning to value the beauty and people of the future over what he had lost to the past. This was even further suggested as the route in an interview made a short time after that episode. Now, it's fair to assume that Genndy changed his mind as time went on, and possibly wanting to surprise fans who had come to expect Jack staying in the future.
Really, he should just make an alternate ending where Aku is killed in the future. Even if it's just as uneven as the ending we got for TV, I think that would at least satisfy some of the people who wanted to see Jack let go of his past in every sense of the word.