The tool for this is called preferences; people need to somehow express their preferences for/against the side effects in monetary terms and then economists have the tools to factor them in. Everybody can make a gut decision about the severity of side effects, but economists are the professionals who at least attempt to do this empirically.
They're kinda waiting for progress of philosophy and psychology here because these areas of research so far fail to be helpful enough.
Nevertheless; an example: Economists know three kinds of "best" tax systems. The "first best" requires so much information that only god could do it. The "second-best" is still impractical. The "third best" is what economists seek; it's at least meant to minimise the net damage of externalities.
Some taxes have huge side effects (income tax was estimated at up to 30% additional costs for the society in an American study during the 90's), while others have only negligible side effects (such as coffee tax, a tax that requires almost no effort because at one stage coffee is in a bottleneck and very easily taxed).
The idea is to balance the taxes so that the side effects in % are roughly the same.
This needs to be seen in context of pigou taxes and political intentions (such as fairness), of course.
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