I couldn't quite answer the question as posed, but thanks to John Griesmer's hint I managed to get a positive answer with slightly different (and perhaps more 'natural') hypotheses, so I will put something here so that the question doesn't remain unanswered.
Claim: Let $X$ be a compact zero-dimensional space, let $S \subseteq \mathrm{Homeo}(X)$ and let $U$ be a clopen subset of $X$. Suppose that $S^{-1}:=\{s^{-1} \mid s \in S\}$ is equicontinuous on $Y = \overline{SU}$. Then $\{sU \mid s \in S\}$ is finite.
Proof: We regard $S^{-1}$ as a family of functions from $Y$ to $X$ by restricting the domain. This family of functions is equicontinuous and uniformly bounded, so by the Arzelà–Ascoli theorem (see e.g. Willard, General Topology, Theorem 43.15), $S^{-1}$ has compact closure in $C(Y,X)$. We then have a continuous map $\theta$ from $C(Y,X)$ to $C(Y,\mathbb{R})$ given by $\theta(f)= 1_{U} \circ f$, so $\theta(S^{-1})$ has compact closure in $C(Y,\mathbb{R})$. Since elements of $\theta(S^{-1})$ only take values in $\{0,1\}$, $\theta(S^{-1})$ is discrete in $C(Y,\mathbb{R})$, hence finite. Finally $\theta(S^{-1})$ coincides with the subset $\{1_{sU} \mid s \in S\}$ of $C(Y,\mathbb{R})$, so $\{sU \mid s \in S\}$ is finite.