Hey there,
Your Natal Plums look alive and happy. Have you tried to get some side-branching going? Or what is your plan for them? What size are they to become?
As for re-potting: No. Don't. The plants have just rooted. They will need a couple of weeks to grow roots that are strong enough, otherwise they may break off. So leave them there a little while longer. the stems being in the ground is not an issue; It is the depth at which you potted them for rooting.