To show that the square commutes we need to prove $\neg \circ \top = \bot$.
Consider this diagram:
$$ \begin{CD} 0@>0_1>>1 @>!_1>> 1 \\
@V{!_0}VV@V{\bot}VV @VV{\top}V \\
1 @>>\top>\Omega @>>{\neg}> \Omega\end{CD}$$
The right square is the pullback that defines $\neg$, as the characteristic arrow of $\bot$. The left square is a pullback that defines $\bot$, as the characteristic arrow of $0_1$, the unique arrow from the initial object. (The square is flipped diagonally.) By the pasting lemma, the whole rectangle is a pullback. The composition along the bottom must be the characteristic arrow of $!_0 = 0_1$, which is $\bot$, and we end up with the desired $\neg\circ \top = \bot$.
So the square commutes in any topos where $\bot$ exists (where arrows from the initial object are monic). We did not use $\Omega \simeq 1 + 1$ yet.
To show that this is in fact a pullback is a bit harder. We need the fact that toposes are extensive categories, and this is not entirely trivial to prove.
Specifically, in an extensive category, we have that for "double square" diagrams such as the one below, if the bottom row is a coprodcut, the top row is a coproduct iff both squares are pullbacks
$$ \begin{CD} 1@>\top >> \Omega @<\bot<< 1\\
@V{1}VV@V{\neg}VV @VV{1}V \\
1 @>>\bot>\Omega @<<{\top}< 1 \end{CD}$$
It is at this point where we use the assumption that $\Omega \simeq 1 + 1$, and, as a result, the left square is a pullback (which is the pullback you wanted). The right square is also a pullback, but that is just the definition of $\neg$.
It may be provable without the extensive property, if anyone knows, please comment.