The reason it's best to kill off Pa before Clark becomes Superman is precisely
because of all the things you listed there. There
should be a pang of tragedy about the fact that Jonathan Kent never got to meet Lois or his grandson or have any kind of relationship with them. It
should sting a little that Jonathan Kent was one of the primary factors in making Kal-El of Krypton into not only Clark Kent of Smallville, but Superman, the World's Greatest Hero. Yet he doesn't get to live to see all his work come to fruition.
Because life isn't always fair. Nobody gets everything they want. Even Superman. Especially Superman. And that is an extremely important lesson for Superman to learn.
However, the great thing is by splitting the difference and keeping Ma Kent alive, you can get literally EVERYTHING you would get by keeping Pa Kent alive without that oh-so-important lesson that makes Superman work so much better than he does with Ma & Pa both being around.
She can have that relationship with Lois.
She can be the world's most adorable grandma to Jonathan Samuel Kent. She gets to feel that pride that she and her beloved late husband raised the world's greatest hero.
It's perfectly understandable for fans to be protective of the characters they love. They don't want anything bad to ever happen to them. They want them to be happy. They want things to always work out for them. But that's not how good drama works. There's a reason the symbol for drama is this:
and not just this:
You need both happiness and sadness to make the character work, particularly one as idealized and perfect as Superman. Without that tragedy and loss, beyond simply being from a dead world, the bright and hopeful optimism and hope Superman represents doesn't shine as bright because it's based upon no real foundation of real pain that the character has had to overcome. It's one of the reasons Batman and Spider-Man resonate so well with people. Beyond the powers and gadgets and costumes, great superheroes draw in audiences because under all the crazy awesome stuff, there's some real sadness to it all that makes it all work.