It's not difficult at all with a slim PS2. x_X All that you need to do is tape down a few buttons inside the console; you're not risking anything unless you're very stupid, or very clumsy.
I think some of the horror stories that you've heard are probably due to the crappiness of the early model lasers. I remember that when the swap trick was first being used with slim PS2s, people's consoles were dying in droves, and some people blamed the trick itself (as if a few bits of sellotape could actually cause that much damage). It eventually emerged that it was just that the early model slimlines had incredibly dodgy lasers.
As for your 'not a PS2 disc' message, does it happen with all games, or just a few? Are they games that you've been able to boot before? I know that certain games (Suikoden III, Xenosaga II, Wild ARMs IV and V, a bunch of others) require a double swap using a utility like DVDLoader, or else they'll give you a 'not a valid disc' message.