Let me start by giving the multiplication table for $\mathbf{S}_7$ for future reference.
\begin{array}{c|ccccccc}
\cdot &1 &2 &3 &4 &5 &6 &7\\
\hline
1 &1 &3 &2 &7 &6 &5 &4\\
2 &3 &2 &1 &6 &7 &4 &5\\
3 &2 &1 &3 &5 &4 &7 &6\\
4 &7 &6 &5 &4 &3 &2 &1\\
5 &6 &7 &4 &3 &5 &1 &2\\
6 &5 &4 &7 &2 &1 &6 &3\\
7 &4 &5 &6 &1 &2 &3 &7
\end{array}
The following might not be the ideal solution, but for want of a more elegant one, here it goes...
Following the reasoning advanced in the post, it is enough to show that if $\theta$ is a congruence of $\mathbf{S}_7^2$ such that $\langle a,b \rangle \theta \langle c,d \rangle$, with $a \neq c$ and $b \neq d$, then $\theta = \nabla_{S_7^2}$.
Since such congruence has to have, in each of its classes, one element from each row and column (thinking of the elements of $\mathbf{S}_7^2$ in a matrix), it is enough to show that
$$\Theta(\langle 1,1 \rangle, \langle 2,b \rangle) = \nabla_{S_7^2},$$
whenever $b \neq 1$ (if $b = 1$ this would be $\ker\pi_2$).
So let us see that for each such $b$, we still have two elements of the same column in the same class, thus obtaining a contradiction.
If $\langle 1,1 \rangle \;\theta\; \langle 2,2 \rangle$, then
$$
\begin{cases}
\langle 1,1 \rangle \cdot \langle 1,4 \rangle \;\theta\; \langle 2,2 \rangle \cdot \langle 1,4 \rangle\\
\langle 1,1 \rangle \cdot \langle 2,5 \rangle \;\theta\; \langle 2,2 \rangle \cdot \langle 2,5 \rangle
\end{cases}
\Rightarrow
\begin{cases}
\langle 1,7 \rangle \;\theta\; \langle 3,6 \rangle\\
\langle 3,6 \rangle \;\theta\; \langle 2,7 \rangle
\end{cases}
\Rightarrow \langle 1,7 \rangle \;\theta\; \langle 2,7 \rangle,
$$
a contradiction.
If $\langle 1,1 \rangle \;\theta\; \langle 2,3 \rangle$, then
$$
\begin{cases}
\langle 1,1 \rangle \cdot \langle 1,4 \rangle \;\theta\; \langle 2,3 \rangle \cdot \langle 1,4 \rangle\\
\langle 1,1 \rangle \cdot \langle 2,6 \rangle \;\theta\; \langle 2,3 \rangle \cdot \langle 2,6 \rangle
\end{cases}
\Rightarrow
\begin{cases}
\langle 1,7 \rangle \;\theta\; \langle 3,5 \rangle\\
\langle 3,5 \rangle \;\theta\; \langle 2,7 \rangle
\end{cases}
\Rightarrow \langle 1,7 \rangle \;\theta\; \langle 2,7 \rangle,
$$
a contradiction.
If $\langle 1,1 \rangle \;\theta\; \langle 2,4 \rangle$, then
$$
\begin{cases}
\langle 1,1 \rangle \cdot \langle 1,2 \rangle \;\theta\; \langle 2,4 \rangle \cdot \langle 1,2 \rangle\\
\langle 1,1 \rangle \cdot \langle 2,5 \rangle \;\theta\; \langle 2,4 \rangle \cdot \langle 2,5 \rangle
\end{cases}
\Rightarrow
\begin{cases}
\langle 1,3 \rangle \;\theta\; \langle 3,6 \rangle\\
\langle 3,6 \rangle \;\theta\; \langle 2,3 \rangle
\end{cases}
\Rightarrow \langle 1,3 \rangle \;\theta\; \langle 2,3 \rangle,
$$
a contradiction.
If $\langle 1,1 \rangle \;\theta\; \langle 2,5 \rangle$, then
$$
\begin{cases}
\langle 1,1 \rangle \cdot \langle 1,2 \rangle \;\theta\; \langle 2,5 \rangle \cdot \langle 1,2 \rangle\\
\langle 1,1 \rangle \cdot \langle 2,4 \rangle \;\theta\; \langle 2,5 \rangle \cdot \langle 2,4 \rangle
\end{cases}
\Rightarrow
\begin{cases}
\langle 1,3 \rangle \;\theta\; \langle 3,7 \rangle\\
\langle 3,7 \rangle \;\theta\; \langle 2,3 \rangle
\end{cases}
\Rightarrow \langle 1,3 \rangle \;\theta\; \langle 2,3 \rangle,
$$
a contradiction.
If $\langle 1,1 \rangle \;\theta\; \langle 2,6 \rangle$, then
$$
\begin{cases}
\langle 1,1 \rangle \cdot \langle 1,2 \rangle \;\theta\; \langle 2,6 \rangle \cdot \langle 1,2 \rangle\\
\langle 1,1 \rangle \cdot \langle 2,7 \rangle \;\theta\; \langle 2,6 \rangle \cdot \langle 2,7 \rangle
\end{cases}
\Rightarrow
\begin{cases}
\langle 1,3 \rangle \;\theta\; \langle 3,4 \rangle\\
\langle 3,4 \rangle \;\theta\; \langle 2,3 \rangle
\end{cases}
\Rightarrow \langle 1,3 \rangle \;\theta\; \langle 2,3 \rangle,
$$
a contradiction.
If $\langle 1,1 \rangle \;\theta\; \langle 2,7 \rangle$, then
$$
\begin{cases}
\langle 1,1 \rangle \cdot \langle 1,2 \rangle \;\theta\; \langle 2,7 \rangle \cdot \langle 1,2 \rangle\\
\langle 1,1 \rangle \cdot \langle 2,6 \rangle \;\theta\; \langle 2,7 \rangle \cdot \langle 2,6 \rangle
\end{cases}
\Rightarrow
\begin{cases}
\langle 1,3 \rangle \;\theta\; \langle 3,5 \rangle\\
\langle 3,5 \rangle \;\theta\; \langle 2,3 \rangle
\end{cases}
\Rightarrow \langle 1,3 \rangle \;\theta\; \langle 2,3 \rangle,
$$
a contradiction.
Update (Trying to follow the comment of Keith Kearnes.)
Let $\mathbf{G}$ be the group of automorphisms of $\mathbf{S}_7$ which fix $1$ and $2$ (and also $3$, since $1 \cdot 2 = 3$).
Then $\mathbf{G}$ acts transitively on $\{4,5,6,7\}$ (we may consider the automorphisms given by $(45)(67)$, $(46)(57)$ and $(47)(56)$).
Now we can reduce the last four cases to a single one, like this:
If $\langle 1,1 \rangle \,\theta\, \langle 2, \phi(4) \rangle$, where $\phi \in G$, then
$$\langle 1,1 \rangle \cdot \langle 1,2 \rangle \;\theta\; \langle 2, \phi(4) \rangle \cdot \langle 1,2 \rangle,$$
that is, $\langle 1,3 \rangle \,\theta\, \langle 3, 2 \cdot \phi(4) \rangle$.
On the other hand,
$$\langle 1,1 \rangle \cdot \langle 2, 1 \cdot (2 \cdot \phi(4)) \rangle \;\theta\; \langle 2, \phi(4) \rangle \cdot \langle 2, 1 \cdot (2 \cdot \phi(4)) \rangle,$$
that is, $\langle 3, 2 \cdot \phi(4) \rangle \,\theta\, \langle 2, \phi(4) \cdot (1 \cdot (2 \cdot \phi(4))) \rangle$.
Now it is an easily verifiable fact of the Fano plane (see connection with $\mathbf{S}_7$ here; also in the beginning of Keith Kearnes' answer), that if $\{u,v,uv\}$ is a line, and $x \notin \{v,uv\}$, then $u(vx) = (uv)x$, whence
$$x(u(vx))=uv.$$
In particular, since $1 \cdot 2 = 3$, we have $x(1(2x))=3$, whenever $x \in S_7 \setminus \{2,3\}$, yielding $\phi(4) \cdot (1 \cdot (2 \cdot \phi(4))) = 3$, and therefore, $\langle 1,3 \rangle \,\theta\, \langle 2,3 \rangle$, a contradiction.