As I understood it, the pci-e slot's plastic cover came off, so the card it'self is fine.
If you cut the pins, so that they can't anymore touch each other, you pretty much cause said PCI-E slot to be unusable.
On other hand, re-attaching the plastic cover is likely impossible so as a quick fix, yes.. I would say cut them.
MB should work normally after that if no other damage was done.