Here's the full combinatorial argument. Raney's lemma was about half of it, I'd say. The argument shows that $S(n,2) = \binom{3n-1}{n} \frac{3}{3n-1}$ (which is equivalent to the two formulations I give in the question). At the end I'll discuss the generalization to the $r$ case.
Intro.
Consider the sequences with $2n$ occurrences of $-1$ (i.e., $2n$ heads) and $n$ occurrences of $+2$ (i.e., $n$ tails). We want to show that the number of these sequences with all partial sums nonzero is $\binom{3n-1}{n} \frac{3}{3n-1}$. The complete sum and empty sum are clearly $0$, so "partial sum" excludes those two cases. The sequences we want to count can be split into three groups: (1) all partial sums positive, (2) all partial sums negative, (3) some partial sums positive and some negative.
Group 1: The number of these sequences with all partial sums positive is $\binom{3n-1}{n} \frac{1}{3n-1}$.
This is the part that uses Raney's lemma. If all partial sums are positive, the last element in the sequence must be $-1$. Thus we want to count the number of sequences with $2n-1$ occurrences of $-1$ and $n$ occurrences of $+2$ that add to $+1$ and have all partial sums positive. Ignoring the partial sums restriction, there are $\binom{3n-1}{n}$ such sequences. If we partition these $\binom{3n-1}{n}$ sequences into equivalence classes based on cyclic shifts, Raney's lemma says that exactly one sequence in each equivalence class has all partial sums positive. Because there are $3n-1$ elements in each sequence there $3n-1$ sequences with the same set of cyclic shifts, and so there are $3n-1$ sequences in each equivalence class. Thus the number of sequences in Group 1 is $\binom{3n-1}{n} \frac{1}{3n-1}$.
Group 2: The number of these sequences with all partial sums negative is also $\binom{3n-1}{n} \frac{1}{3n-1}$.
To see this, just reverse the sequences counted in Part 1.
Group 3: The number of these sequences with some positive partial sums and some negative partial sums is, yet again, $\binom{3n-1}{n} \frac{1}{3n-1}$.
This one is a little trickier. First, because of the $-1$'s, it is not possible to switch from positive partial sums to negative partial sums. Thus any sequence counted here must have exactly one switch: from negative partial sums to positive partial sums. The switch must occur at some point where the partial sum is $-1$ and the next element is $+2$. Thus we have some sequence $(a_1, \ldots, a_m, +2, a_{m+2}, \ldots, a_n)$ where the sums $a_1, a_1 + a_2, \ldots, a_1 + \ldots + a_m$ are all negative. Consider the sequence $(+2, a_m, \ldots, a_2, a_1, a_{m+2}, \ldots, a_n)$. Since $+2 + a_m + \ldots + a_1 = 1$, and $a_k + a_{k-1} + \ldots + a_1 < 0$ for all $k$, $1 \leq k \leq m$, it must be the case that $+2 + a_m + \cdots + a_{k+1} > 1$ for all $k$, $1 \leq k \leq m-1$. So the sequence $(+2, a_m, \ldots, a_2, a_1, a_{m+2}, \ldots, a_n)$ is in Group 1. To see that this mapping is a bijection, note that any sequence in Group 1 must start with $+2$ and have a first time that a partial sum is equal to $+1$. Thus this transformation is reversible.
Summing up.
Putting Groups 1, 2, and 3 together we see that the total number of sequences we want to count is $\binom{3n-1}{n} \frac{3}{3n-1}$.
Generalization to the $r$ case.
The arguments for Group 1 and Group 2 adapt in a straightforward manner for general $r$; we get $\binom{(r+1)n-1}{n} \frac{1}{(r+1)n-1}$ for both. Sequences in Group 3 can still only switch once - from negative partial sums to positive partial sums. But Group 3 can be broken up into subgroups depending on whether the first partial sum to become positive is $+1, +2, \ldots, r-1$. Using transformations like the one described above for Group 3 in the $r = 2$ case, we can show that there is a bijection between each of these $r-1$ subgroups and Group 1. Thus there are $\binom{(r+1)n-1}{n} \frac{r-1}{(r+1)n-1}$ sequences in Group 3. In total, then, $S(n,r) = \binom{(r+1)n-1}{n} \frac{r+1}{(r+1)n-1}$.
Final comment.
All of this is may be easier to visualize in terms of paths from $(0,0)$ to $((r+1)n,(r+1)n)$ that use right steps of size $1$ and up steps of size $r$ and that do not step on the diagonal except at $(0,0)$ and $((r+1)n,(r+1)n)$. (They can cross the diagonal, though.) I found it easier to discuss the partial sums interpretation, though, given the difficulty of creating such graphics on this forum.
Best Answer
Here is a combinatorial proof that $$ \binom{2n}{n} - C_n = \sum_{k=1}^n \frac12\binom{2k}{k} C_{n-k}. $$ Since $C_n = \frac{1}{n+1}\binom{2n}{n}$, the left-hand side simplifies to $n C_n$, and after multiplying by $2$, this gives us the equation you want.
Both sides of the equation above are going to count walks of length $2n$ that start and end at $0$, but do dip below the $x$-axis. Since $\binom{2n}{n}$ counts the total number of walks that start and end at $0$, and $C_n$ counts the number that don't dip below the $x$-axis, the number we are counting is $\binom{2n}{n} - C_n$.
Now split these walks up into $n$ classes based on the last step at which the walk goes from $-1$ to $0$. Such a step must exist, because once we dip below the $x$-axis, we have to come back up to $0$ at some point.
The number of walks in which this step is the $(2k)^{\text{th}}$ step is exactly $\frac12 \binom{2k}{k} C_{n-k}$:
Summing over all values of $k$, we get the right-hand side of the equation above.