The manual also says remove the brakes but I've never seen anyone do that, and I've been told it is not necessary......
To mash the axle I'm guessing a rubber mallet?
Yeah, well, they want you to take your mufflers off to get the rear wheel off

If the way you have your bike jacked up makes it easy enough for you to slide the wheel
back in and get both rotors back into both calipers at the same time, there should be no need to
take the calipers off. If it makes it easier to take the calipers off, put the wheel on, and then slide
each caliper down onto its rotor, do that... I don't think I take the calipers off...
Anywho... whether it makes it easier for someone to take the fender/calipers/whatever off
to get the job done, I think the real important things are the orders of tightening the nuts
and bolts that hold your wheel on, and the pumping of the forks at the right time to get stuff
seated right. And if you get done and your axle is sticking out a little like the one in the picture -
you're not done

I think I tightened the axle bolt enough to pull it all the way through last time I did it. And
if I remember, the axle bolt is not the first thing the manual sez to tighten, so I loosened
it after the axle was where I wanted it to be, and then tightened everything in the order
the manual specifies...
-Mike