Mercury was believed to have some beneficial qualities before its side effects were known. I don't know enough about it to say at what dosages it become toxic or how much makes it cumulative... so maybe those eye ointments and vaccines have levels that are actually safe, but everyone is jumping on the anti-mercury bandwagon, throwing out the baby with the bathwater.
Of course it's SOP to take drugs that are harmful off the market. I don't know what precautions are taken or not taken to prevent this harm, but nothing in life is 100% safe... the FDA trials do involve animal models and then limited use in study groups before putting drugs on the market.
Questioning is fine, but living in constant paranoia is unwarranted. In the end, you put faith in some source of information anyway, whether it be the FDA, JAMA, Paul Chek, or what your mother taught you. Look, you take part in MT fights that carry increased risk of all sorts of serious injuries compared to if you didn't fight, but you do it regardless, right? Same thing with medicines. They have immediate effects. Antibiotics cure infections. Lipitor lowers your cholesterol levels. Insulin controls your blood sugar levels. NSAIDs reduce inflammation. These are not subjective effects, and these are desirable effects. Do they have side effects? Probably. You decide which of these problems you'd rather endure when weighed against possible side effects. Getting in your car to go to the mall, even though it's one of the leading causes of death. Life is a gamble.
Are some of these treatable with other, "natural" approaches? Perhaps many are, but in my opinion, these approaches are even less documented, so who knows what risks you are taking with them too.
Time magazine had an interesting article this week about risk assessment of americans... mentioned the same things - people who are afraid of flying, so they take to the roads, even though they put themselves in higher risk of dying that way... people protesting in front of nuclear plants, but hardly in front of tobacco plants, even though many more people die from smoking than radiation.