Note that the partial fractions decomposition of the inverse
of the Rising Factorial gives:
$$
\eqalign{
& \left( {x - 1} \right)^{\,\underline {\, - \left( {m + 1} \right)\,} } = {1 \over {x^{\,\overline {\,m + 1\,} } }}
= {{\Gamma (x)} \over {\Gamma (x + m + 1)}} = \;\quad \left| {\;0 \le {\rm integer }\, m} \right.\quad = \cr
& = \sum\limits_{0\, \le \,k\, \le \,m} {{1 \over {x + k}}\left( {{{\left( { - 1} \right)^{\,k} } \over {\left( {m - k} \right)!k!}}} \right)}
= \sum\limits_{0\, \le \,k\, \le \,m} {{1 \over {x + k}}\left( {{{\left( { - 1} \right)^{\,k} } \over {m!}}\binom{m}{k}
} \right)} \cr}
$$
So
$$
\eqalign{
& \sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,k} \right)} {\left( { - 1} \right)^{\,j} \binom{k}{j}
{1 \over {2n + 2j + 1}}} = \cr
& = {1 \over 2}\sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,k} \right)} {\left( { - 1} \right)^{\,j} \binom{k}{j}
{1 \over {\left( {n + 1/2 + j} \right)}}} = \cr
& = {{k!} \over {2\left( {n + 1/2} \right)^{\,\overline {\,k + 1\,} } }} \cr}
$$
We have then that the sum in $n$ is
$$
\eqalign{
& S(k) = \sum\limits_{0\, \le \,n} {\left( { - 1} \right)^{\,n} \sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,k} \right)} {\left( { - 1} \right)^{\,j} \left( \matrix{
k \cr
j \cr} \right){1 \over {2n + 2j + 1}}} } = \cr
& = {1 \over 2}\sum\limits_{0\, \le \,n} {\left( { - 1} \right)^{\,n} {{k!} \over {\left( {n + 1/2} \right)^{\,\overline {\,k + 1\,} } }}} = \cr
& = {1 \over {2\left( {k + 1} \right)}}\sum\limits_{0\, \le \,n} {\left( { - 1} \right)^{\,n} {{1^{\,\overline {\,k + 1\,} } }
\over {\left( {1 + n - 1/2} \right)^{\,\overline {\,k + 1\,} } }}} = \cr
& = {1 \over {2\left( {k + 1} \right)}}\sum\limits_{0\, \le \,n} {\left( { - 1} \right)^{\,n} {{1^{\,\overline {\,n - 1/2\,} } }
\over {\left( {2 + k} \right)^{\,\overline {\,n - 1/2\,} } }}} = \cr
& = {{1^{\,\overline {\, - 1/2\,} } } \over {2\left( {k + 1} \right)\left( {2 + k} \right)^{\,\overline {\, - 1/2\,} } }}
\sum\limits_{0\, \le \,n} {\left( { - 1} \right)^{\,n} {{\left( {1/2} \right)^{\,\overline {\,n\,} } } \over {\left( {3/2 + k} \right)^{\,\overline {\,n\,} } }}} = \cr
& = {{\Gamma \left( {1/2} \right)\Gamma \left( {2 + k} \right)} \over {2\left( {k + 1} \right)\Gamma \left( 1 \right)\Gamma \left( {3/2 + k} \right) }}
\sum\limits_{0\, \le \,n} {\left( { - 1} \right)^{\,n} {{\left( {1/2} \right)^{\,\overline {\,n\,} } } \over {\left( {3/2 + k} \right)^{\,\overline {\,n\,} } }}} = \cr
& = {{\Gamma \left( {1/2} \right)\Gamma \left( {1 + k} \right)} \over {2\,\Gamma \left( {3/2 + k} \right)}}{}_2F_{\,1} \left( {\left. {\matrix{
{1/2\;,\;1} \cr
{k + 3/2} \cr
} \;} \right| - 1} \right) = \cr
& = 2^{\,2\,k} {{\left( {k!} \right)^{\,2} } \over {\left( {2k + 1} \right)!}}\;\;{}_2F_{\,1} \left( {\left. {\matrix{
{1/2\;,\;1} \cr
{k + 3/2} \cr
} \;} \right| - 1} \right) \cr}
$$
where in the mid of the derivation we have used the identity
$$
{{z^{\,\overline {\,w\,} } } \over {\left( {z + a} \right)^{\,\overline {\,w\,} } }} = {{z^{\,\overline {\,a\,} } } \over {\left( {z + w} \right)^{\,\overline {\,a\,} } }}
$$
and at the end the duplication formula for Gamma
$$
\Gamma \left( {2\,z} \right) = {{2^{\,2\,z - 1} } \over {\sqrt \pi }}\Gamma \left( z \right)\Gamma \left( {z + 1/2} \right) = 2^{\,2\,z - 1} {{\Gamma \left( z \right)\Gamma \left( {z + 1/2} \right)} \over {\Gamma \left( {1/2} \right)}}
$$
Alternative Approach
Actually there is a more straight alternative aproach through the Digamma Function
$$
\eqalign{
& S(k) = \sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,k} \right)} {\left( { - 1} \right)^{\,j} \left( \matrix{
k \cr
j \cr} \right)\sum\limits_{0\, \le \,n} {\left( { - 1} \right)^{\,n} {1 \over {2n + 2j + 1}}} } = \cr
& = \sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,k} \right)} {\left( { - 1} \right)^{\,j} \left( \matrix{
k \cr
j \cr} \right)\sum\limits_{0\, \le \,m} {\left( {{1 \over {4m + 2j + 1}} - {1 \over {4m + 2j + 3}}} \right)} } = \cr
& = {1 \over 4}\sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,k} \right)} {\left( { - 1} \right)^{\,j} \left( \matrix{
k \cr
j \cr} \right)\sum\limits_{0\, \le \,m} {\left( {{1 \over {m + j/2 + 1/4}} - {1 \over {m + j/2 + 3/4}}} \right)} } = \cr
& = {1 \over 4}\sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,k} \right)} {\left( { - 1} \right)^{\,j} \left( \matrix{
k \cr
j \cr} \right)\left( {\psi \left( {j/2 + 3/4} \right) - \psi \left( {j/2 + 1/4} \right)} \right)} = \cr
& = {1 \over 4}\sum\limits_{\left( {0\, \le } \right)\,j\,} {\left( \matrix{
k \cr
2j \cr} \right)\left( {\psi \left( {j + 3/4} \right) - \psi \left( {j + 1/4} \right)} \right) - \left( \matrix{
k \cr
2j + 1 \cr} \right)\left( {\psi \left( {j + 5/4} \right) - \psi \left( {j + 3/4} \right)} \right)} = \cr
& = {1 \over 4}\sum\limits_{\left( {0\, \le } \right)\,j\,} {\left( \matrix{
k + 1 \cr
2j + 1 \cr} \right)\psi \left( {j + 3/4} \right) - \left( \matrix{
k \cr
2j \cr} \right)\psi \left( {j + 1/4} \right) - \left( \matrix{
k \cr
2j + 1 \cr} \right)\psi \left( {j + 1 + 1/4} \right)} = \cr
& = {1 \over 4}\sum\limits_{\left( {0\, \le } \right)\,j\,} {\left( \matrix{
k + 1 \cr
2j + 1 \cr} \right)\left( {\psi \left( {j + 3/4} \right) - \psi \left( {j + 1/4} \right)} \right) - \left( \matrix{
k \cr
2j + 1 \cr} \right){1 \over {j + 1/4}}} \cr}
$$
Since we can write (re. for instance to this page)
$$
\eqalign{
& \psi \left( {j + 3/4} \right) = 4\sum\limits_{0\, \le \,l\, \le \,j - 1\,} {{1 \over {4\,l + 3}}} + {\pi \over 2} - \ln 8 - \gamma
= \psi \left( {j + 3/4} \right) - \left( {\psi \left( {3/4} \right) - \left( {{\pi \over 2} - \ln 8 - \gamma } \right)} \right) \cr
& \psi \left( {j + 1/4} \right) = 4\sum\limits_{0\, \le \,l\, \le \,j - 1\,} {{1 \over {4\,l + 1}}} - {\pi \over 2} - \ln 8 - \gamma
= \psi \left( {j + 1/4} \right) - \left( {\psi \left( {1/4} \right) - \left( { - {\pi \over 2} - \ln 8 - \gamma } \right)} \right) \cr}
$$
we arrive to express the sum as
$$
\eqalign{
& S(k) = \sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,k} \right)} {\left( { - 1} \right)^{\,j} \binom{k}{j}
\sum\limits_{0\, \le \,n} {\left( { - 1} \right)^{\,n} {1 \over {2n + 2j + 1}}} } = \cr
& = {1 \over 4}\sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,k} \right)} {\left( { - 1} \right)^{\,j} \binom{k}{j}
\left( {\psi \left( {j/2 + 3/4} \right) - \psi \left( {j/2 + 1/4} \right)} \right)} = \cr
& = {\pi \over 4}2^{\,k} - 2\sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,k} \right)\,} {\binom{k+1}{2j+1}
\left( {\sum\limits_{0\, \le \,l\, \le \,j - 1\,} {{1 \over {\left( {4\,l + 3} \right)\left( {4\,l + 1} \right)}}} } \right)}
- \sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,\left( {k - 1} \right)/2} \right)\,} {\binom{k}{2j+1}{1 \over {4j + 1}}} = \cr
& = {\pi \over 4}2^{\,k} - 2\sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,k} \right)\,} {\binom{k+1}{2j+1}
\left( {\sum\limits_{0\, \le \,l\, \le \,j - 1\,} {{1 \over {\left( {4\,l + 2} \right)^{\,2} - 1}}} } \right)}
- \sum\limits_{\left( {0\, \le } \right)\,j\,\left( { \le \,\left( {k - 1} \right)/2} \right)\,} {\binom{k}{2j+1}{1 \over {4j + 1}}} \cr}
$$
Interesting the comparison of this expression with the one given by
@robjohn