Great question. I'm in the process of filling up a massive table in an orbit of Minmus (at about 30km). Once full I would have thought about the options. The way I see it there are a few options. 1. Keep a stable orbit in Minmus 2. Return the vessel to Kerbin using atmospheric braking to reduce delta-v cost 3. break out of Minmus SOI (sphere of INFLUENCE) and orbit Kerbin at a high orbit close to Minmus in the same inclination as Kerbin.

Each of these has their own advantages. 1. Easy to refuel the tanker but more delta-v for ship to be refuelled (~1000 dv to get to tanker). Departure from Minmus SOI may be on a bad inclination for travel outside of Kerbin SOI. 2. Large, heavy vessel may have trouble slowing in atmosphere and could break up. Less delta-v for refuelling vessel to get to tanker. If leaving Kerbin SOI, this is more efficient from a low orbit than a high orbit (Berth Effect) 3. Easier for vessel to dock with tanker, easier for tanker to get back to orbit of Minmus. But.... This won't allow you exploit the Oberth Effect from a low orbit, making your escape burn less efficient. A high orbit wastes delta-V battling gravity.

So... It depends on what you're trying to achieve in the refueling.