trying to remove rear axle

[Fazerider]

+1 for taking the weight off the axle, wedge a couple of bits of wood under the wheel to do that if you're working alone.
Penetrating oil may help. Your idea of a sacrificial bolt in the hollow end of the axle to protect it while you drift it out is a good one.
The bearings shouldn't suffer any ill-effects as the race inners are all braced against each other with spacers.