I would get the biggest pot you could find to move it into, which will give the
roots more room to grow.
I would also remove all of the current soil, and replace it with cool
compost from plants, without manure or hot compost so it won't burn the tree, if you have it, which will give the plants a lot of nutrients it will need to help naturally fight off the diseases. You could buy an organic compost soil if needed.
If you have a way to catch and collect rainwater to
water the tree with, that would be best, as tap water is probably treated with chemicals that will generally kill most soil life. It can be best to not overwater, as wet feet can stress the
apple tree and make it more succeptible to diseases.
Do you know what variety the apple tree is? Certain ones can be more susceptible to diseases than others. Also depending on your location certain disease pressures can be higher.
I hope this helps a little!