Yes, learning GUI driven analysis programs like MorphoJ is somewhat easier to use initially. Particularly if all you ever need is the functionality offered in the package. The main catch is, the moment you need something else you are stuck. It is also much more challenging to export data from those kinds of tools, if you need to generate publication quality images. reformat tables etc… So there are drawbacks to both approach.
You don’t necessarily learn to program in R, if all you all you do is to use a package like geomorph. You replace teaching keyboard shortcuts and menu selections with function names and parameters to pass them, which the student can learn to program if they choose to so in future. But you dont necessarily need to learn to program anything in R. Just learn function names and be able to write things in a script. It is a bit more upfront investment, but in the long run it pays off, particularly for students.
Going back to your original inquiry, I see morphoJ takes a text input (but they provide no description of what fields are necessary). Probably that would be your simplest option. If you get an example of what that looks like, we can help you to reformat the fcsv into that.