Regarding Potential Risks Vs Potential Benefits In Medicine

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If there is a treatment that has moderately healing effects (by no means miraculous, but enough to provide some relief to the problem being treated) on, say, 990 out of 1000 people and severely damaging effects causing great suffering on, say, 10 out of 1000 people, is it more important to better the lives of those 990, or is it more important to protect those 10 people from severe harm?

[I apologize if this isn't well-phrased.]

Are you talking about a prophylactic treatment, like a vaccine, or a treatment for an established illness? In either case, it depends on whether the people who benefit and the people who are at risk are the same (ie, is everyone equally likely to be vulnerable to the condition, or are some people more vulnerable than others?), on the severity of the disease in question, and on the severity of the risks in question.

There is NO medicine without side effects. Tylenol is one of the most lethal drugs in our current pharmacopia, but it's still considered safe enough (and the analgesic/febrifugic effects beneficial enough) to sell cheaply over the counter.

1% having serious side effects is a pretty damn high when it only gives relief. Honestly, it's hard to paint with a broad brush on this, I would want to know the specifics.

It depends on things like the other available treatments, the severity of the condition, whether we can identify who suffers side effects, the magnitude of the effects and side effects, the cost of the treatment, and treatments for the side effects.