This is not an answer, but it's too long for a comment: I'm going to show that the OP's conjecture is true in some (admittedly, rather special) cases. It is hoped that this will help to find a counterexample, if any exists.
Given a (multiplicatively written) semigroup $S$ and elements $a, b \in S$, denote by $R_S(a,b)$ the set of all pairs $(x,y) \in S \times S$ such that $x,y \notin \{a, b\}$ and $ax = by$, and let $r_S(a,b)$ be the largest integer $m \ge 0$ for which there exist $(x_1, y_1), \ldots, (x_m, y_m) \in R_S(a,b)$ with $x_i \ne x_j$ and $y_i \ne y_j$ for all $i,j \in [\![1,m]\!]$ with $i \ne j$. Next, define the invariant
$$
r(S) := \sup \{r_S(a,b): a, b \in S \text{ and } a \ne b\},
$$
where $\sup \emptyset := 0$. The OP's conjecture can then be reformulated as follows:
Conjecture. If $S$ is a commutative, finite semigroup of order $n \ge 2$ other than the cyclic monoid/group of order $3$, then $r(S) \ge \lfloor (n-1)/2 \rfloor$.
This is not exactly the original conjecture, as it is not restricted to
semigroups of order $n \ge 4$. However, the conjecture (in its new formulation) is clearly true for $n = 2$, as in this case $r(S) = \lfloor (n-1)/2 \rfloor = 0$. On the other hand, it is just tedious to check (see my other non-answer here) that the only order-$3$ exception to the conjecture is the cyclic group of order $3$ (which indeed is an exception, as pointed out by Fabius Wiesner in the comments). Lastly, let me say a few words about commutativity.
Remark. If $S$ is a left zero semigroup (meaning that $xy = x$ for all $x, y \in S$), then it is fairly obvious that $r(S) = 0$. That is, the conjecture fails for left zero semigroups of order $\ge 3$. This demonstrates that the conjecture does not carry over to the non-commutative setting, which counters a certain halo of arbitrariness in its current formulation and supports the restriction to the commutative setting.
Here is a summary of what's coming next (all relevant definitions will be given in due course):
- Proposition 1 is about monoids (of order $\ge 3$) whose group of units is non-trivial.
- Proposition 2 is about non-unital cyclic semigroups.
- Proposition 3 is about nilsemigroups.
To start with, recall that an element $a$ in a semigroup $S$ is cancellative if left and right multiplication by $a$ are both injective functions on $S$. Let me first show that we can get rid of semigroups that have more than one cancellative element.
Lemma. If a semigroup $S$ has a cancellative element $a$ of finite order, then $S$ is a monoid and $a$ is one of its units. Conversely, every monoid has a cancellative element of finite order (that is, the identity.)
Proof. This is a standard exercise. Since $a$ has finite order in $S$, there exist $m, n \in \mathbb N^+$ with $m < n$ such that $a^m = a^n$. Set $e := a^{n-m}$. By cancellativity), $a = a^{n-m+1} = ae = ea$. It follows that, for every $x \in S$, $ax = aex$ and $xa = xea$, which, again by cancellativity, yields $x = ex = xe$. So, $S$ is a monoid and $e$ is its identity element. Accordingly, $e = a^{n-m}$ implies that $a$ is a unit (its inverse in $S$ being $a^{n-m-1}$, which is equal to $e$ when $n = m+1$). []
Based on the lemma, we can focus our attention on three classes of semigroups: those with no cancellative elements, the monoids whose only unit is the identity, and the monoids with non-trivial units. Our first proposition shows that the OP's conjecture is true for the last class.
Proposition 1. Let $S$ be a finite monoid of order $n \ge 3$ but not a cyclic group of order $3$, and suppose, in addition, that $S$ has at least one non-trivial unit. Then $r(S) \ge n-\varepsilon$, where $\varepsilon$ is either $2$ or $3$, depending on whether $S$ has a unit of order $2$ or not, respectively. In particular, $S$ satisfies the OP's conjecture.
Proof. By hypothesis, $S$ is a finite monoid whose group of units is non-trivial. So, let $a$ be a unit of $S$, other than the identity $1_S$, that has minimal order in $S$. Let $a^{-1}$ be the inverse of $a$. Given $y \in S$, we have $a^{-1} y = 1_S$ iff $y = a$, and $a^{-1} y = a$ iff $y = a^2$. Since $(a^{-1}y, y) \in R_S(a, 1_S)$ for all $y \in S$ and left multiplication by $a^{-1}$ is an injective function on $S$, this yields $r(S) \ge r_S(a, 1_S) \ge n-\varepsilon$: in fact, if $a$ has order $2$ (that is, $a^2 = 1_S$), then $r_S(a,1_S) = n-2$; otherwise, $r_S(a, 1_S) \ge n-3$.
Now, if $n = 3$, then the order of $a$ in $S$ is necessarily equal to $2$ (or else $S$ is a cyclic group of order $3$), and hence $r(S) = 3-2 = \lfloor (3-1)/2 \rfloor = 1$. Otherwise, $r(S) \ge n-3 \ge \lfloor (n-1)/2 \rfloor$. In any case, $S$ satisfies the OP's conjecture. []
In the next proposition, we will consider the case when the semigroup $S$ is cyclic, meaning that there exists an element $g \in S$ such that, for every $x \in S$, one has $x = g^k$ for some $k \in \mathbb N^+$.
Proposition 2. If $S$ is a finite, cyclic semigroup of order $n \ge 3$ but not a monoid, then $r(S) = n-2$ and hence $S$ satisfies the OP's conjecture.
Proof. As $S$ is a cyclic semigroup but not a monoid, we gather from the structure theorem of finite cyclic semigroups (see, for instance, Proposition 1.1 in the 2016 edition of Benjamin Steinberg's Representation Theory of Finite Monoids) that there exist an element $g \in S$ and a minimal positive integer $m \le n$ such that $g^m = g^{n+1}$ and the following condition holds:
$\text{(C)}$: $g^i = g^j$, for some $i, j \in [\![1, n]\!]$, if and only if (i) $i = j$ or (ii) $i, j \ge m$ and $i \equiv j \bmod d$, where $d := n-m+1$.
Set $a := g^\mu$ and $b := g^n$, where $\mu := \max(1,m-1)$. Since $n \ge 3$, it is clear from $\text{(C)}$ that $a \ne b$. In addition, for each $i \in [\![1,n]\!]$, we have $bg^i = g^{n+i} = g^{m+i-1} = ag^i$. It follows that $(x,x) \in R_S(a,b)$ for all $x \in S$, and hence
$$
r(S) \ge r_S(a,b) \ge n-2 \ge \lfloor (n-1)/2 \rfloor.
$$
We are thus done, as it is obvious that $r(S) \le n-2$. []
For the last proposition of this post, recall that a semigroup $S$ is nilpotent, or a nilsemigroup, if there is a (provably unique) element $0_S \in S$, called the zero of $S$, such that every $x \in S$ has a power $x^k$ (with $k \in \mathbb N^+$) equal to $0_S$.
Proposition 3. If $S$ is a finite nilsemigroup of order $n \ge 3$, then $r(S) = n-2$ and hence $S$ satisfies the OP's conjecture.
Proof. Let $0_S$ be the zero element of $S$. Since $S$ is finite, it satisfies the descending chain condition on principal right ideals (that is, on subsets of the form $\{a\} \cup aS$); and since $S$ has more than one element, this implies that there exists a maximal left divisor $a$ of $0_S$ in $S \setminus \{0_S\}$, where 'maximal' means that every left divisor of $0_S$ that is left divided by $a$ is either $0_S$ or $a$. It follows that $aS = \{0_S\}$; otherwise, $a = ax$ for some $x \in S$, and hence $0_S \ne a = ax^k$ for all $k \in \mathbb N^+$, which is however impossible because $S$ is nilpotent. Consequently, $(x,x) \in R_S(a,0_S)$ for every $x \in S$ and hence
$$
r(S) \ge r_S(a,0_S) \ge n-2 \ge \lfloor (n-1)/2 \rfloor.
$$
That is enough to conclude (cf. the last line of the proof of Proposition 2). []