I have to say I agree with Painteds---most, but not all reptiles carry salmonella (I think the figure I read is something like 90%), which is a bacteria shed (not secreted) from the intestine when a turtle is stressed or ill. A turtle does not "lose" its bowels (like from fear), the bacteria just comes out with the poop.
Tests for salmonella are notoriously inaccurate, because a seemingly healthy turtle may actually be carrying the bacteria but it may not be present in a stool sample. And I do believe that there is a tipping point with the amount of salmonella a turtle carries; go over the tipping point, and the salmonella bacteria will make a turtle ill (I've never heard of it aiding with digestion).
Aside from the obvious precaution of washing hands after handling a turtle and objects in the tank, keeping a turtle healthy with a good diet and enclosure is also important.
If the water level isn't really deep, gloves can be useful (I sometimes use disposable ones). I've noticed gloves with extra-long sleeves sold in aquarium shops. Nets with extra long handles can also help retrieving and positioning objects as well.
I wouldn't get paranoid about getting salmonella, just take common-sense precautions and you should be fine.
