The reason vinegar ruins the naked egg is that the vinegar moves into the egg by osmosis. That's a function of time and of concentration. The longer the egg soaks, the more acid it absorbs. I haven't tried this variation of the experiment yet, but I've made a naked egg for non-cooking purposes. I've been thinking how to do this, and here's what I've got:
1) Use a more concentrated vinegar to weaken the shell faster, so it doesn't soak as long. Be prepared to remove most of the shell by hand when it's weak enough. The egg's membranes should hold up fine if you're careful.
2) Once the shell is sufficiently compromised to allow expansion, try soaking it in distilled (or highly purified) water. The egg will expand, and that should counter some of the osmotic pressure, keeping the vinegar out. It will also make removing shell pieces by hand easier.
Expect it to take a few days. Also, I don't know if you're using supermarket eggs or something sturdier, but the shells on most supermarket eggs are thinner to begin with. I wouldn't try this on a free-range egg from your henhouse.