Samba works perfectly between MOS on Pegasos and AmigaOS. I use it on a daily basis. No worries there. FTP is a little faster though and would be better for transferring huge files, but its nowhere near as versatile as samba.
And a PCMCIA network card is about the only way you'll get a network card for an A1200. There are two other options - one is a zorro daughterboard and a zorro network card. You'd need to put your A1200 in a tower case for this. This is not recommended because zorro cards are very hard to find these days and haven't aged well.
Then there's a PCI daughterboard and a PCI network card. This is expensive but will give you the best performance. You'll need a tower case for this as well.
IMO, unless you're planning on spending a *lot* of money souping up the Amiga, the PCMCIA way is the best way. And since you're not going to tower up your Amiga, it's the only way.