First some general remarks. You're asking whether $S/R$ is free as a $R$-module. If $S$ is a $R$-algebra which is free of finite rank, then the map $R \to S$ splits as a map of $R$-modules. This fact was already noticed by Florian Eisele in his answer to the other MO question.
Now for an explicit counter-example to your question. Consider the ring $R={\bf Z}[x,y,z]/(x^2+y^2+z^2-1)$. It is an integral domain. It is known that there exists a $R$-module $M$ which is not free such that $R \oplus M \cong R^3$. For a nice construction, see e.g. Keith Conrad's notes. Explicitly we can take $M=\{(f,g,h) \in R^3 : xf+yg+zh=0\}$. Note that we can embed $M$ in $R^2$ by $(f,g,h) \mapsto (f,g)$, and the cokernel $R^2/M$ is a torsion module, so there exists $F \in R \backslash \{0\}$ such that $F \cdot R^2 \subset M$.
Now, we would like to construct a $R$-algebra structure on $R \oplus M$. We can do this by considering the $R$-algbera $S_0 = R \otimes_{\mathbf{Z}} \mathcal{O}$ where $\mathcal{O}$ is an order of a cubic field $K$. It is an integral domain, since the polynomial $x^2+y^2+z^2-1$ is irreducible over any field of characteristic not $2$. Let $(1,\alpha,\beta)$ be a $\mathbf{Z}$-basis of $\mathcal{O}$. Embed $R \oplus M$ in $S_0$ by $(f,(g,h)) \mapsto f+g\alpha+h\beta$. This won't be a subring of $S_0$ in general, but $S=R \oplus FM$ is a subring of $S_0$ since $(FM) \cdot (FM) \subset F^2 S_0 \subset R \oplus FM$. So we have constructed an integral domain $S$ over $R$ such that $S/R \cong M$ is not free over $R$.
I don't know whether it's possible to find a counterexample where $R \to S$ splits as a map of rings, in other words where $S=R \oplus I$ where $I$ is an ideal of $S$.