I like all of the ideas put forth. The two part resin is bullet proof but requires some technique to get right. Wax is easy and can be done regularly. CA is an awesome finish for pens and other objects human beings handle routinely, but as @talkers says isn’t real fun to apply, especially if you don’t like the fumes. Regular old varnish would probably work, too. I like EEE, too as it seems to be pretty durable as well. I finish a lot of pens with it.
I don’t think it being food safe is as important as say a cutting board, but many finishes are food safe in the bottle stopper context. Like @bertberaht says though shellac is a very bad idea as alcohol ruins the finish.
Something I used to recommend at Rockler, when I worked there, is to take a piece of wood, preferably of the same variety, and finish it with a particular finish to see if you like it. This was usually in reference to larger projects than a bottle stopper, but the principle still applies. This way you’ll have an idea of what the finished product will look like. If you go to Rockler, there is a guy there named Dan who is an expert in finishing. He will be happy to help you and show you some alternatives.