I have some wires that were originally pulled through a wall from a junction box to an outlet. The drywall is off the wall right now and I'm doing some work on the wiring. Would best practice be to staple the wires inside the wall or is that going to make it harder for someone in the future to replace the wire in the wall?
Wiring is stapled or otherwise fastened to protect it from damage, such as from fasteners used to hang decorations on the wall. You should staple per NEC guidelines. In your case, it's probably a matter of fastening to studs within a foot of each box.
If you anticipate needing to reconfigure the wiring later, run conduit accordingly.
The junction box is required to be accessible via a plate cover and the wires are required to be secured within 12" of the outlet; both per NEC.