I do think Rumple can be killed by other means than the knife. A nuke for instance would def do the job.
Rumple taught Cora how to pull out hearts in order for her to enact the Dark Curse, but she didn’t. And then she pulled out her own and hid it, probably so that Rumple wouldn’t pull out her heart and control her. So she had to hid it somewhere where Rumple couldn’t get to it.
From what we know so far, the only things that can stop Rumple is the ink and the magical jail bars, at least in FTL. I think it’s more likely she hid it in another universe, that has something similar to the ink/bars but that we haven’t seen yet.