Karl Malone was seemingly the better scorer based on numbers but I don't think the difference is great if Malone was even better at all. Malone got a lot of spoon-fed lay-ups out of the pick-and-roll and he wasn't much of a traditional back-to-the-basket low post scorer just like KG. Later on in his career, when he didn't scorer out of the pick-and-roll or at the free throw line, it was the mid range jumper from the extended free throw line. KG has never been a very good low post scorer either, but he could score without the benefit of the pick-and-roll since he had face-up skills and the ability to score off the dribble out of a face-up position. Karl Malone put up better scoring numbers, but I don' think there's a huge difference in ability to score.
Malone was obviously stronger and tougher. But pretty much every other advantage belongs to KG. At KG's peak, he did bulk up to be closer to 250 than the 220 he was early on in his career. And at that peak, KG was one of the most well-rounded and versatile players ever.
I'd take KG at his peak over Malone at his.