You're right, this is basically a Lowenheim-Skolem result.
The "pruning" process you've described comes equipped with a rank function from $T$ to the order of $T$ together with $\infty$:
If $\sigma\in T^\zeta$ but not $T^{\zeta+1}$, then $rk(\sigma)=\zeta$.
If $\sigma\in T^\xi$ for all $\xi$ (that is, if it lasts until the process stabilizes), then $rk(\sigma)=\infty$.
This rank function, in turn, gives us a family of unary predicates naming each "stage": consider the structure $$\mathcal{T}=(T; <, (U_\zeta)_{\zeta\in order(T)\cup\{\infty\}})$$ where $<$ is the tree order on $T$ and each $U_\zeta$ is a unary predicate naming $\{\sigma\in T: rk(\sigma)=\zeta\}$.
The structure $\mathcal{T}$ captures the tree structure and the pruning process; and if the order of $T$ is countable, then the language of $\mathcal{T}$ is also countable. So by Lowenheim-Skolem $\mathcal{T}$ has a countable elementary submodel, with underlying tree $S$. The key question now is:
Can you show that the order of $S$ is the same as that of $T$?
HINT: The order of a tree is the supremum of the non-$\infty$ ranks of its nodes. So by induction, can you show that the $S$-rank of a node $\sigma\in S$ is the same as the $T$-rank of $\sigma$? Certainly the $S$-rank can't exceed the $T$-rank, so it's enough to show that $S$ doesn't "kill nodes prematurely" . . .