Edit. I think I was able to prove it using the nerve complex that Andy Putman suggested below. Here is what I have. The part about retracting simplices down I feel is correct, but perhaps I have not expressed it rigorously enough. Any feedback on this proof would be much appreciated.
Applying Borsuk's nerve theorem to Andy Putman construction and observations,$\Delta_n$ is homotopy equivalent to the simplicial complex $X_n$ whose vertex set is $[n]$ and in which a subset $J\subseteq [n]$ is a face if and only if $J$ is coprime-free. We also know that $X_n$ has $C(n)+2$ connected components, $C(n)+1$ of which are singletons. The nontrivial connected component, call it $X_n'$, consists of all primes in the range $[2,n/2]$ as well as all composite numbers in $[n]$. The claim is that $X_n'$ is contractible.
We will construct the deformation retraction to a single point in steps. First note that the set $V_2$ all even vertices, viewed as a subcomplex of $X_n'$, is a simplex, so we may retract this down to a point without altering the homotopy of $X_n'$. Call this point $\bar 2$. Now in this new complex, consider the set $V_3$ of all vertices whose smallest prime divisor is $3$ ($V_3$ includes all remaining multiples of $3$, since all multiples of $6$ were retracted to the point $\bar 2$). The subcomplex on $V_3\cup \{\bar 2\}$ is a simplex, since in the original complex $X_n'$, the set of vertices divisible by $3$ was a simplex, and all we have done is retract some subsimplex consisting of vertices divisible by $6$ to a point, call it $\bar 3$. The same will be possible when we define the set $V_5$ of all integers whose smallest prime divisor is $5$, and then consider $V_5\cup \{\bar 3\}$. Continuing this reasoning, we may perform a retraction for every prime $p\in [2,p/2]$ until all we are left with is a single point.