The author seems to describe very carefully what it means for a collection of pairs to "determine" a relation. You start with a relation that you know is an equivalence relation, and then start throwing things out until you cannot throw out anymore.
For instance, if you begin with the relation
$$
R = \{(1,1), (2,2), (3,3), (2,3), (3,2)\}
$$
Then you can throw out $(2,2)$ and $(2,3)$ and only keep $(3,2)$
$$
R' = \{(1,1), (3,3), (3,2)\}
$$
because once you know $(3,2) \in R$, you know that $(2,3) \in R$ by symmetry and you know $(2,2) \in R$ by transitivity.
The author seems to arrive at $n/2$ as follows : You need each element of $S = \{1,2,\ldots, n\}$ to be present in some pair. We can order the elements so that
$$
R' = \{(1,2), (3,4), \ldots, (n-1,n)\} \text{ (assume $n$ even for now)}
$$
Now, $|R'| = n/2$, and this is the bare minimum. If any element appears in two pairs, then the element that it "kicked out" would have to show up in another pair, thereby increasing the number of pairs.
One has to make this argument rigorous, but that is the gist of it.