EMC2 uses a Hardware Abstraction Layer (HAL) which is very configurable. You can easily map any signal to any hardware pin, or modify signals with hal components as if they were real analog or digital electronic signals. See SampleParport for an example.
Chapter 6 of the [EMC2 User Manual] is a HAL tutorial that specifically describes how to change the pinout of a parallel-port stepper machine, including the addition of an external ESTOP input. [HTML version]
ClassicLadder, a software PLC, has been added to EMC2. It allows plenty of flexibility for creating custom machine logic, in a format that most integrators are familiar with.