I think you should re-arrange your code to always check the emergency stop input as part of its operation loop. I think this will make your code easier rather than forcing a context change via the interrupt. Your mention of EMERGENCY STOP via the cpu worries me - if this function is to protect life and limb then you are way off the mark. What happens if the cpu fails? The EMERGENCY STOP then fails to operate. EMERGENCY STOP is exactly what it says - emergency! This must cut power to the motors in the most direct and reliable means possible. You can have another pair of contacts going to the cpu to inform it of the action but NEVER rely on the cpu where life and limb are at stake. You would want to comply with the european machineries directive.

Do a google on 'therac 25' - it will explain the follies of relying on the cpu alone.