A. Well, it's not exactly clean. You could pick up germs that would put you at risk for catching things like a cold or flu, but it's not any riskier than using the bathroom like you would normally. The key is keeping your clothes on to minimise contact with bacteria. And since this is a quickie, staying dressed only adds to the hotness.
As for what position to try, standing up doggie-style is easiest, given what little room you have to move. Face away from your partner, palms placed against the stall wall for stability, as he enters you from behind. If you want more leverage, you could try propping up one foot or knee on the toilet seat to help you thrust back onto him. And luckily for your germaphobic boyfriend, this position allows him to keep his hands on your body - and nothing else.