Um - don't confuse a little surface rust with major dammage. If that rust is really bad enough to cause problems with that piston or cylinder then you better toss the engine back into the ocean where you found it.
Seriously, removing one piston just because of a little rust ia not recommended. If you took the head off to do a valve job or replace a head gasket then you'll double or tripple the amount of work just to take the bottom end apart to pop out one piston. That, plus honing just one cylinder is unheard of. Might also have some balancing issues unless you replace all pistons as a set.
Yes, knocking out a piston from the bottom is the typical way to do it.