Yeah, that's a good idea danners, definitely worth breadboarding. I also agree with fourtytwo42 that the MOSFET isn't contributing much; I'd start by feeding the protected signal directly into the MCU. If you're scared of hurting your MCU and want a visual or oscilloscope output, or don't want to code yet, just use some similar logic-level input (buffer, inverter, NAND gate) as a subsitute.
So referring to the circuit diagram, I'd have R1, R2, D1, D3 and R11 in place. Then, the MCU's digital (or analog) input can go directly where U1A is. To add adjustability, I'd add P1 in series with R2, or add it in parallel to D1. Just make sure that D1 and D2 can handle the worst case current (as pointed out by fourtytwo42), build it up on a breadboard, and try it out!
Be wary of this though: D3 will allow a certain amount of charge to flow up to the +5V rail every cycle of the DCC, in other words, it will be pumping a certain current up into the +5V rail. This means that C3 is essential for a start, but it also means that if the other circuitry running off that 5V rail isn't consuming a large amount of current, and if the 5V PSU doesn't support sinking the excess current away, the 5V rail could start rising out of control. This might be a non-issue, or might be something that deserve further protection circuitry (which could be a simple as a big ol' resistor from 5V to ground); only time and/or details calculations will tell. To be fair, this might be an issue with the original circuit, so

By the way, what I'm suggesting is basically exactly the same as what you're suggesting, just to be clear. Your 50k pot would be R2, and R1 + R11 are both just current limiting resistors that can be 10 - 100kiloohms each. You can also try adding a tiny capacitor where C1 is, which would keep noise under control.