Using the Wikipedia notation, the full matrix of transition probabilities is written as
$$P = \left(\begin{array}{cc} Q & R \\ 0 & I \end{array}\right)$$
with the states organized so that the last states are all absorbing. In the OP's example from population genetics, the states would be organized as $1, 2, \ldots, M-1, 0, M$.
If $\tau$ denotes the first time the Markov chain enters the set of absorbing states, the absorption probability for state $k$ given that the Markov chain starts in state $i$ is
$$B_{ik} := P(X_{\tau} = k \mid X_0 = i).$$
Observe that if $X_n = j$ for a transient state $j$ then $\tau > n$, and by the time homogeneity of the Markov chain
$$P(X_{\tau} = k \mid X_n = j) = B_{jk}.$$
From Wikipedia it follows that
$$B_{ik} = (NR)_{ik}.$$
The expected number of visits to state $j$ conditionally on the chain starting in $i$ and being absorbed in $k$ is
$$\xi_{ik}(j) = E\left( \sum_{n=0}^{\infty} 1(X_n = j) \ \middle| \ X_0 = i, X_{\tau} = k\right) = \sum_{n=0}^{\infty} P(X_n = j \mid X_0 = i, X_{\tau} = k) .$$
Now the probabilities in the infinite sum can be rewritten as follows
\begin{align*}
P(X_n = j \mid X_0 = i, X_{\tau} = k) & = \frac{P(X_{\tau} = k, X_n = j \mid X_0 = i)}{P(X_{\tau} = k \mid X_0 = i)} \\
& = \frac{P(X_{\tau} = k \mid X_n = j, X_0 = i)P(X_n = j \mid X_0 = i)}{P(X_{\tau} = k \mid X_0 = i)} \\
& = \frac{P(X_{\tau} = k \mid X_n = j)}{P(X_{\tau} = k \mid X_0 = i)} (Q^n)_{ij} \\
& = \frac{B_{jk}}{B_{ik}}(Q^n)_{ij}.
\end{align*}
From this we obtain the formula
\begin{align*}
\xi_{ik}(j) & = \frac{B_{jk}}{B_{ik}}\sum_{n=0}^{\infty} (Q^n)_{ij}
= \frac{B_{jk}}{B_{ik}}N_{ij},
\end{align*}
where the absorption probabilities $B_{ij}$ and $B_{ik}$ can be computed from $N$ and $R$ using the formula above.
