USB will generally just fail/lock up. If you do get problems with that, get a USB isolator.
Search ebay for "USB Isolator", and get one that uses an ADUM chip (I think most of them do).

However, it sounds like you have a noise problem.
Simple fix is to add a small capacitor to the E-stop input to the controller to act as a basic noise filter, but depending on your e-stop circuit, it may be better to add a resistor to increase the load on the circuit so noise isn't as big a problem.
The only concern with those fixes is, the noise may be affecting other things, but not as noticeably I.e. lost/gained steps.