First, I think that you are missing a factor of $2$ somewhere. The correct result is
$$|\nu - \mu| = \frac12 \sup_f \bigg| \int f d(\nu - \mu) \bigg |.$$
The proof I know of this goes through another characterisation of the total variation distance given by Scheffe's lemma.
Scheffe's Lemma: Fix a reference measure $m$ such that there are measurable $g,h: \Omega \to [0,\infty)$ such that $d\mu = g dm$ and $d \nu = h dm$. Then
$$|\nu - \mu| = \frac12 \int |g-h| dm.$$
Note that requiring the existence of a reference measure is no real imposition. Radon-Nikodym means you can always just take $m = \frac12 ( \mu + \nu)$.
Given this characterisation, the remaining inequality is straightforward. Indeed,
\begin{align}
\bigg |\int f d(\nu - \mu) \bigg | =& \bigg|\int f (g-h) dm \bigg |
\\ \leq& \int |f| |g-h| dm
\\ \leq& \int |g-h| dm
= 2 |\nu - \mu|
\end{align}
for any $f$ with $\|f\|_\infty \leq 1$.
Here is a direct proof based on your idea to use the Hahn decomposition that doesn't use Scheffe's lemma. Let $A^+ = \{f \geq 0\}$ and $A^- = \{f < 0\}$. Further, set $\lambda = \nu - \mu$.
We can decompose $\bigg |\int f d\lambda\bigg|$ as
\begin{align}
\bigg | \int_{E^+ \cap A^+} f d\lambda + \int_{E^+ \cap A^-} f d\lambda + \int_{E^- \cap A^+} f d\lambda + \int_{E^- \cap A^-} f d\lambda \bigg |
\end{align}
The advantage of this decomposition is that we know the signs of each of the terms and so, splitting terms into groups based on their sign, we get
\begin{align}
\bigg |\int f d\lambda\bigg| \leq& \bigg | \int_{E^+ \cap A^+} f d\lambda + \int_{E^- \cap A^-} f d\lambda \bigg | \\ +& \bigg |\int_{E^+ \cap A^-} f d\lambda + \int_{E^- \cap A^+} f d\lambda \bigg|
\\ = &\int_{E^+ \cap A^+} f d\lambda + \int_{E^- \cap A^-} f d\lambda
\\- & \bigg(\int_{E^+ \cap A^-} f d\lambda + \int_{E^- \cap A^+} f d\lambda \bigg)
\end{align}
Now, the worst case for bounding each of these terms occurs when $f$ is $1$ or $-1$ depending on the set we integrate over. For example,
$$\int_{E^+ \cap A^+} f d\lambda \leq \int_{E^+ \cap A^+} 1 d\lambda = \lambda(E^+ \cap A^+)$$
Similarly,
\begin{align}
\int_{E^- \cap A^-} f d\lambda \leq &\int_{E^- \cap A^-} -1 d\lambda \leq -\lambda(E^- \cap A^-)
\\
\int_{E^+ \cap A^-} f d\lambda \geq& \int_{E^+ \cap A^-} -1 d\lambda = -\lambda(E^+ \cap A^-)
\\
\int_{E^- \cap A^+} f d\lambda \geq & \int_{E^- \cap A^+} 1 d\lambda = \lambda(E^- \cap A^+)
\end{align}
Plugging all of these bounds in and using additivity of the measures to combine terms and get rid of the $A$s, we get that
$$\bigg|\int f d\lambda \bigg| \leq \lambda(E^+) -\lambda(E^-) \leq 2 |\nu - \mu|$$
as desired.
For completeness, what follows is a proof of the other inequality with the factor of $\frac{1}{2}$ present based on the idea of Hahn-decomposition. Note that for an arbitrary measurable set $A$, $|\lambda(A)| = |\lambda(A^c)|$ since $\lambda(\Omega) = 0$.
Hence $|\lambda(A)| = \frac12 (|\lambda(A)| + |\lambda(A^c)|)$. We can then write
\begin{align}
|\lambda(A)| \leq& \frac12 [ \lambda(A \cap E^+) - \lambda(A \cap E^-) + \lambda(A^c \cap E^+) - \lambda(A^c \cap E^-)] \\=&
\frac12 (\lambda(E^+) - \lambda(E^-))
\\=& \frac12 \bigg|\int 1_{E^+} - 1_{E^-} d \lambda \bigg|
\\ \leq& \frac12 \sup_f \bigg |\int f d\lambda \bigg |
\end{align}
which proves the other inequality.