Marlin/RAMPS is a 3D printer controller that happens to have the bare-minimum functionality to control a simple 3- or 4-axis mill or router. MachineKit is a full-featured motion control
platform that is hugely flexible/extensible and was built around serious CNC mill control applications.
This is kind of like asking, "I need to kill a really big spider. Should I grab a flyswatter or hire a tactical mercenary team?"
Marlin will barely get the job done. It's designed for something else. MachineKit is exceptionally capable of doing the job, but is way more than you need for a MPCNC. Where MachineKit will be a really good choice is if you want to do everything with the machine -- mill, 3d print, control coolant spray, run a plasma torch, whatever. (Honestly though, if that's your goal, you ought to be building something a hell of a lot sturdier than a MPCNC.)
If you haven't bought anything yet, and only want to mill, I'd recommend TinyG. That's generally the platform of choice for small mill/router projects.