The biggest problem I see with your little tree is a nutrient deficiency. That happens when iron (or another nutrient) is either missing or unavailable to plants. Chlorosis in apple trees can be caused by too alkaline soil (what is your water pH?), the soil is too wet or compacted, herbicide damage or other nutrient deficiencies.
When you say you fertilize once in awhile, what do you use and how much? When is the last time you repotted? The soil is very low in the pot. How wet is the soil? Does the pot drain poorly?
I don't see a problem with cutting the main leader out. It is an apple tree, the leader is always removed at some point. I don't see signs of apple scab either.
Your tree is fixable, we just need to fix out what the fix might be.