This sounds like a project I could love. Will you be sanding and staining or painting the desk? I like the plexiglass idea if you are refinishing it but if not, you may not like looking at the top surface if it's worn. Unless you like that look. Formica counter top material cleans up well, too. Sometimes you can find smaller remnant type pieces at the big box stores. My sewing machine counter and cutting table are formica. I had them made to size with a rolled edge. Much easier on the arms when resting against the edges to sew.
Good luck and post pics of your finished project!