"All the available pins" is a very large number. You would spend more on the protection circuit than on the Due itself.
The basic principle of protection is to protect any wire that leaves or enters your box. Establish a safe perimeter, then you don't need to protect every individual wire inside.
The second basic principle is that you can't protect against everything. Any time you make something "foolproof" you just discover that there is a bigger fool. Natural disasters like lightning also fit into this category. The best you can hope for if your box is struck by lightning is that it doesn't set fire to anything else.
The Due chip already has protection diodes on every input and output pin. It would be damaged by static electricity if it wasn't protected like this.
Professional circuit-protection designers are always looking at the energy in each "oops!" event. A car battery hooked up backwards has enough energy to burn a hundred Arduino Due's. A static zap from walking on nylon carpet doesn't really have a lot of energy, even if it is 15KV. Most protection circuits are designed to absorb energy so you need to know how much energy is in each type of event that the circuit has to deal with.
So back to the perimeter protection. What kinds of things are likely to happen? The biggest one for me is hooking up power backwards. That depends on the plugs you use. If you're powered from USB then it's extremely unlikely that you'll get the power reversed. So I don't put that kind of protection on USB lines. If you've got bare wires hooked up to a car battery, then you'll get it backwards in about 1 out of 5 attempts. So definitely do include protection for that.
For most inputs and outputs a simple 1K resistor is an exceptionally good protection device. You can't easily push enough energy through the 1K resistor to damage the Due on the other end. Whatever does get through can be handled by the protection diodes built into the chip.
However high-speed data lines and power can't be protected with a resistor. USB, SPI and so on. My go-to device is the TVS diode. This is like a zener diode but with a much sharper switch-on voltage. you can even get neat little packages like the TPDE2E001DZDR which will protect two 5V data lines and a power line.