My bad and apologies for misinterpreting. That said, a shield still seems more appropriate for the application you're describing. Protecting inputs seems like a better use of board space for beginners. But opinions are free to differ. Fwiw, I find it easier to debug via the serial channel since it allows me to not only debug inputs and outputs, but also review responses to same.
Imo, an inexpensive way to implement what you're describing is using an RBBB with a breadboard and LEDs on the channels in question. Makes for an easy development environment and insures that one keeps track of the channels being used.
I too like to use LEDs to keep track of certain channels (serial, among others) in boards i design but certainly not all channels. At some point it becomes confusing to have tons of channels blinking.