Hi Mnis,
You're right if the machine is actually moving. But if it's not doing anything I don't see a reason why it needs a restart. Now there are two safety jumpers (at least on my ultimaker 3, but I think the pcb hasn't change much over the 2 version). There's no need for 2 of those (if you need more emergency stops you could put them in serie). So if one would be a hard stop, the other could be a soft one (an actual pause pin). That would make it easy to add an end of filament warning system for example.
Regards,
David