Enemies can die on the spikes, and this would'nt count as a failure for Pacifist. Remember to don't use windmill box near witch for Good ending's leaf placement

Can you get pacifist achievement on a new game + save file when you didn't do the first part as pacifist ? I'm assuming yes .

The answer is yes ;) Got Pacifist on my hard New Game + !

There's a point in the Forlorn Monestary where you literally can't progress without killing some of the falling enemies on spikes, so if this was a problem nobody could legitimately earn the achievement because you wouldn't be able to get the key needed to progress to the krest piece there. You'll know the point when you see it. It's a good place to collect munny if you have the magnet stone and the amulet if you need some.