This is not an answer but rather extended commentary on Tom
Bachmann's answer. I hope to
address some of Jon's comments on that answer.
Bar constructions with respect to coproducts compute pushouts
First let me address Tom's point (3), that an instance of the
two-sided bar construction computes pushouts. This is probably
well-known but I had to think about it for a bit, so I'll include an
explanation in case it helps someone else. Also, this explanation
helps later with coherence issues for maps between simplicial objects.
The two-sided bar construction can be defined very generally, for a
monoid $M$ for some monoidal structure $\otimes$ together with
left and right $M$-modules $L$ and $R$. Now consider the special
case when $\otimes$ is given by the coproduct. In this case, the
monoidal structure on $M$ is unique, given by the fold $M \sqcup M
\to M$, and the module structures on $L$ and $R$ are given simply
by morphisms $M \to L$, $M \to R$. And the claim is that the
geometric realization of the bar construction is simply the pushout of
$R \leftarrow M \to L$.
One way to see that is to consider the functor $b : \mathrm{Span} \to
\Delta^\mathrm{op}$ where $\mathrm{Span} = \{ r \leftarrow m \to l
\}$ and $b(m \to l) = (d_0 : [1] \to [0])$ and $b(m \to r) =
(d_1 : [1] \to [0])$. It's not hard to check that the coproduct-based
bar construction $\mathrm{Fun}(\mathrm{Span}, \mathcal{C}) \to
\mathrm{Fun}(\Delta^\mathrm{op}, \mathcal{C})$ is given by left Kan
extension along this functor $b$. The usual argument about left Kan
extending along the composite $\mathrm{Span} \to \Delta^\mathrm{op}
\to \ast$, shows that a span and its corresponding bar construction
have the same colimit.
Defining the relevant map of simplicial $A$-modules
Instead of trying to check that Tom's maps are compatible with faces
and degeneracies, let's try to build simplicial maps wholesale. I'll
use $F : \mathrm{Mod}_A \to \mathrm{Alg}^{E_n}_{A}$ for the free
$E_n$-$A$-algebra functor defined on $A$-module spectra, and
$U : \mathrm{Alg}^{E_n}_{A} \to \mathrm{Mod}_A$ for the
corresponding forgetful functor.
The key ingredient in Tom's argument is a simplicial $A$-module
$B_{\bullet}$ whose geometric realization is $U(A/\!/\alpha)$, the
underlying $A$-module of the $E_n$-$A$-algebra in Jon's
question. By the previous section, the simplicial
$E_n$-$A$-algebra $\mathcal{B}_{\bullet} :=
\mathrm{Lan}_b(A\overset{\overline{0}}\leftarrow
{E_n}(\Sigma^kA)\overset{\overline{\alpha}}\to A)$ has geometric
realization given by the pushout of that span, $A /\!/ \alpha$.
Since the forgetful functor $U$ preserves geometric realizations,
the simplicial $A$-module $B_{\bullet} := U \circ
\mathcal{B}_{\bullet}$ will have $U(A /\!/ \alpha)$ as geometric
realization.
Now let $C_{\bullet} := \mathrm{Lan}_b(0 \leftarrow \Sigma^k A \to
A)$ be the coproduct-based bar construction in $\mathrm{Mod}_A$. We
want to define a morphism of simplicial $A$-modules $C_{\bullet}
\to B_{\bullet} = U \circ \mathcal{B}_{\bullet}$, or equivalently a
morphism of simplicial $E_n$-$A$-algebras $F \circ C_{\bullet}
\to \mathcal{B}_{\bullet}$. Now, since $F$ is a left adjoint it
preserves the left Kan extension defining $C_{\bullet}$, so $F
\circ C_{\bullet}$ is the bar construction for the span $F(0)
\leftarrow F(\Sigma^k A) \to F(A)$. The following diagram is a
natural transformation between that span and the one defining
$\mathcal{B}_{\bullet}\require{AMScd}$:
$$\begin{CD}
F(0) @<{F(0)}<< F(\Sigma^k A) @>{F(\alpha)}>> F(A) \\
@V{\mathrm{id}}VV @V{\mathrm{id}}VV @V{\mu_A}VV \\
A @<{\bar{0}}<< F(\Sigma^k A) @>{\bar{\alpha}}>> A \\
\end{CD}$$
This map of spans induces a simplicial map between their respective
bar constructions.
The rest of the argument
I think that now the rest of Tom's argument runs fine: let
$B'_{\bullet}$ be the cofibre in simplicial $A$-modules of
$C_{\bullet} \to B_{\bullet}$. Now, without worrying about
compatibility with faces and degeneracies, you can identify for each
$n$ the map $C_n \to B_n$ to describe $B'_n$ and see that
$B'_n$ is $2k$-connective.