[guided]The induction step is designed to remove one row and one column while staying inside the same class of matrices. Suppose column $j$ of $B$ has at most one nonzero entry.
First consider the case where column $j$ has no nonzero entries. Then column $j$ is the zero vector in $\mathbb{Z}^k$. Since the determinant is linear in each column, replacing one column by the zero vector makes the determinant equal to $0$. Thus $\det B = 0$, which is one of the allowed values.
Now suppose column $j$ has exactly one nonzero entry. Let $i \in \{1,\dots,k\}$ be the unique row index with $B_{ij} \neq 0$. Because $B$ is a submatrix of the incidence matrix $M$, every entry of $B$ is $-1$, $0$, or $1$, so this unique nonzero entry satisfies $B_{ij} \in \{-1,1\}$.
Define $B^{(i,j)} \in \mathbb{Z}^{(k-1)\times(k-1)}$ to be the matrix obtained from $B$ by deleting row $i$ and column $j$. This is not an arbitrary smaller matrix: it is exactly the incidence submatrix selected by the row set $R \setminus \{r_i\}$ and the column set $C \setminus \{c_j\}$, with the induced orderings. Therefore the induction hypothesis applies to $B^{(i,j)}$, and gives
\begin{align*}
\det B^{(i,j)} \in \{-1,0,1\}.
\end{align*}
Cofactor expansion along column $j$ has only one surviving term, because all entries in that column except $B_{ij}$ are zero. Hence
\begin{align*}
\det B = (-1)^{i+j} B_{ij} \det B^{(i,j)}.
\end{align*}
The factor $(-1)^{i+j}B_{ij}$ is either $1$ or $-1$, and multiplying an element of $\{-1,0,1\}$ by $1$ or $-1$ keeps it in $\{-1,0,1\}$. Therefore $\det B \in \{-1,0,1\}$ in this case.[/guided]