Yes, with the axle nut removed, the axle should slide right out. Yours is obviously rusted in there. You're doing all you can do short of cutting it inside the swingarm to get the wheel out. But that would wreck the axle, probably some of the spacers too. Keep soaking, pounding, use some heat (heat gun), and hopefully it will break loose. It could take several days or more. If it does start to move out, pound it back in, work it back and forth. As mentioned, get some PB Blaster, it puts Liquid Wrench to shame.