what are your intentions with this tree? you could leave the limb and graft to the central leader. this would save your seedling variety, and still produce a known cultivar. if the seedling proves to be desirable you could then cut the central leader out ....or most likely leave the graft and pruin the unknown seedling limb. if your growing it for rootstock it's plenty big to graft now.

Thanks for the reply!
I don't plan at all on grafting this tree. I want it to continue growing, it will eventually be placed in the ground and be allowed to grow to a full sized tree (as big and unproductive as that may be). I'm just wondering if that will happen quicker if I remove the competing limb, or if I should for some reason leave the competing limb.

I would trim the limb then, if you want to shape into a central leader tree.