Its odd that I know plenty of people who passed with flying colors in Gen Chem. Then got murdered in Orgo even though they had better study habits. Sometimes it's just the class and the material and it depends on what each person excels at. Orgo required a lot of critical thinking as opposed to just memorization at my school, different from your typical gen chem class. Maybe their study habits got stronger and they were more disciplined and spent more time studying, but that doesn't mean you still grasp the material better because for me, gen chem and orgo were two VERY different courses. Do you expect to excel in english because you got an A in math?
Personally, I think it's plenty valid to worry about what type of classes/graduate school you're going to get into when you're in undergrad, when the hell else would you do it?