Is updating/avoiding this splice worth it, and if so, what's the easiest way to plug the hole?
In my opinion it's not worth the effort and cost to re-run the wire. As long as the inline splice is properly connected at B, e.g. using proper wire nuts, it is not considered a major hazard. Even if you "improve" it by a wire directly from A to C, it is likely you have other splices in your other circuit anyway.  

In terms of cover plate vs patching drywall, that's totally up to you. If it's behind furniture, why not simply choose the easier way.