Did you remember to loosen the clamps on the nut side of the bike, while keeping the opposite tight. If the clamp is snugged up over the axle threads it'll be adding pressure to the threads and make them super hard to undo. Bit like trying to undo a fork cap while still clamped tightly in the top triple.
A bit of heat could help as well, but shouldn't need excessive amounts.
You won't be able to push it through from the puller side. The axle is stepped and seats against the spacers in the hub. At a guess it's possible the threads have been crossed up on the nut. May need to cut the nut off and then clean the axle threads up again. Worst case scenario.
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