The problem, as I see it, is you're asking two different questions. And, they don't have the same answer.
As far as protecting the crew, there could conceivably be little med-nano-bots running around in their bodies, making them essentially immune to whatever the worlds have to throw at them, but they won't be perfect - because you just don't know what's out there.
However, you also address the idea of not introducing our own pathogens to them. This cannot be protected against, except through barrier protocols (environmental suits, etc). Even then, you might have problems: with what do you decon the suits before you exit the ship? That very thing might cause problems to your new friends. Heck, the very act of entering their atmosphere with your ship might bring chemicals/substances/spores/whatever to their world for which they are biologically unprepared. (I'm assuming you would *never* dump your sewage on an alien planet - the biological implications of that are horrendous, besides being un-neighborly and smelly.) You can make some good guesses based on atmosphere composition and general compatibility with terran/vilani biology, but you can't make any assumptions.