"so far as...it" is a parenthetical phrase, which is a phrase that gives more information about a noun or another phrase.
A parenthetical phrase should come after the noun it modifies, so a pronoun like "it" will usually refer to the last word before the parenthetical phrase. In this case, "it" refers to "damnation".
"Gold, if you can find it, is nice to have." It=gold
"My father, if he can be called that, was never home." He=my father; that=the title "father"
This parenthetical phrase is difficult to understand because we do not use "so far as" anymore. It means "to the extent" or "in the way of" or "about".
"The weather, so far as it damages crops, is bad." The weather is not bad in every way, but it is bad regarding crop damage.
"The weather, so far as it damages crops, is bad, but, so far as it keeps mice away, is good." The weather is good and bad, but for different reasons.
In your quotation, the word "damnation" is extremely strong. It is hyperbole. The author is using a parenthetical expression to modify/explain the hyperbole. The explanation allows the author to retain the strength of the hyperbole without sounding unreasonable. The explanation says, "it's not real/literal/complete damnation, it's as much damnation as society can create".
"The curse, so far as the cold and hail can be called that, of the weather came every spring." Is the weather really a curse? Well, not completely, but the cold and hail are like a curse...