Wait for it to grow. Oh, and lose the saucer - you don't need it outdoors and you never want potted plants to sit in puddles.

Over time the trunk will look less awkward. It may have been cut a little short, and there were not sufficient buds to create branches in more of a vase shape.

The main branch will become the new leader, despite the angle. Any pruning style you decide to use will be based on how you treat the leader.

The roots will take care of themselves shortly.

If it was a regular peach, I would prune out the bottom part of the v. Not familiar with dwarf bonanza except that it is super small and more bush than tree in form.

While the shape is not spectacular, it is not a huge concern on fruit trees since they are not shade trees. The fruit is what everyone is after so being perfectly straight is not a big problem. Some of my ugliest fruit trees I ever planted turned out really nice after planting and growing for a few years.

Thanks guys. So those two branches will be the leader branches and should never be cut them?

It's hard to tell where the graft is. Since Bonanza is a miniature, if those two are coming from the graft site, you are stuck with that shape.
If not and the leader is also Bonanza, you could encourage more sprouts to balance it out.

Carla in Sac