When we got the pics of Rumple stabbing Pan didn’t the description of what was going on say that Rumple comes up and the others seem to get frozen, and then after they’re unfrozen Belle falls down crying? So perhaps Rumple gets his powers back by the time he stabs Pan if he’s the one who freezes them. It could be Pan who does it but I think from the description he was caught off guard by Rumple so maybe not.
Although would LOVE it if Rumple stabs him while he’s still magic-less. It would show him being brave and strong and selfless without magic, which would be pretty awesome and empowering considering he’s always been a coward without it.