Starting from the following equations
$$
\begin{align}
\frac{\partial b_{s}\left(t\right)}{\partial t}+\frac{\Gamma_{s}}{2} b_{s}\left(t\right) & =-i\kappa_{1}b_{i}^{\dagger}\left(t\right)+\sqrt{\gamma_{s}}b_{s}^{\text{in}}\left(t\right) \\
\frac{\partial b_{i}^{\dagger}\left(t\right)}{\partial t}+\frac{\Gamma_{i}}{2} b_{i}^{\dagger}\left(t\right) & =i\kappa_{1}b_{s}\left(t\right)+\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(t\right)
\end{align}
$$
perform the Fourier transform and note that $\frac{\partial}{\partial t} \rightarrow -i \omega$ (by properties of Fourier transforms).
$$
\begin{align}
-i\omega b_{s}\left(\omega\right)+\frac{\Gamma_{s}}{2} b_{s}\left(\omega\right) & =-i\kappa_{1}b_{i}^{\dagger}\left(\omega\right)+\sqrt{\gamma_{s}}b_{s}^{\text{in}}\left(\omega\right) \\
-i\omega b_{i}^{\dagger}\left(\omega\right)+\frac{\Gamma_{i}}{2} b_{i}^{\dagger}\left(\omega\right) & =i\kappa_{1}b_{s}\left(\omega\right)+\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(\omega\right)
\end{align}
$$
$$
\begin{align}
\left(\frac{\Gamma_{s}}{2}-i\omega \right) b_{s}\left(\omega\right) & =-i\kappa_{1}b_{i}^{\dagger}\left(\omega\right)+\sqrt{\gamma_{s}}b_{s}^{\text{in}}\left(\omega\right) \\
\left(\frac{\Gamma_{i}}{2} -i\omega \right)b_{i}^{\dagger}\left(\omega\right) & =i\kappa_{1}b_{s}\left(\omega\right)+\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(\omega\right)
\end{align}
$$
Now, solving for $b_{i}^{\dagger}\left(\omega\right)$ in the second equation and substituting into the first, one obtains
$$
\left(\frac{\Gamma_{s}}{2}-i\omega \right) b_{s}\left(\omega\right) =-\frac{i\kappa_{1}}{\left(\frac{\Gamma_{i}}{2} -i\omega \right)}\left(i\kappa_{1}b_{s}\left(\omega\right)+\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(\omega\right)\right)+\sqrt{\gamma_{s}}b_{s}^{\text{in}}\left(\omega\right)
$$
$$
\left(\frac{\Gamma_{s}}{2}-i\omega \right) b_{s}\left(\omega\right)+\frac{i\kappa_{1}\left(i\kappa_{1} b_{s}\left(\omega\right)\right)}{\left(\frac{\Gamma_{i}}{2} -i\omega \right)} =-\frac{i\kappa_{1}}{\left(\frac{\Gamma_{i}}{2} -i\omega \right)}\left(\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(\omega\right)\right)+\sqrt{\gamma_{s}}b_{s}^{\text{in}}\left(\omega\right)
$$
$$
\left(\left(\frac{\Gamma_{s}}{2}-i\omega \right) +\frac{i\kappa_{1}\left(i\kappa_{1} \right)}{\left(\frac{\Gamma_{i}}{2} -i\omega \right)}\right) b_{s}\left(\omega\right)=-\frac{i\kappa_{1}}{\left(\frac{\Gamma_{i}}{2} -i\omega \right)}\left(\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(\omega\right)\right)+\sqrt{\gamma_{s}}b_{s}^{\text{in}}\left(\omega\right)
$$
$$
\left(\left(\frac{\Gamma_{s}}{2}-i\omega \right) -\frac{\kappa_{1}^{2}}{\left(\frac{\Gamma_{i}}{2} -i\omega \right)}\right) b_{s}\left(\omega\right)=-\frac{i\kappa_{1}}{\left(\frac{\Gamma_{i}}{2} -i\omega \right)}\left(\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(\omega\right)\right)+\sqrt{\gamma_{s}}b_{s}^{\text{in}}\left(\omega\right)
$$
$$
\frac{1}{\left(\frac{\Gamma_{i}}{2} -i\omega \right)}\left(\left(\frac{\Gamma_{s}}{2}-i\omega \right)\left(\frac{\Gamma_{i}}{2} -i\omega \right) -\kappa_{1}^{2}\right) b_{s}\left(\omega\right)=-\frac{i\kappa_{1}}{\left(\frac{\Gamma_{i}}{2} -i\omega \right)}\left(\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(\omega\right)\right)+\sqrt{\gamma_{s}}b_{s}^{\text{in}}\left(\omega\right)
$$
$$
\left(\left(\frac{\Gamma_{s}}{2}-i\omega \right)\left(\frac{\Gamma_{i}}{2} -i\omega \right) -\kappa_{1}^{2}\right) b_{s}\left(\omega\right)=-i\kappa_{1}\left(\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(\omega\right)\right)+\sqrt{\gamma_{s}}\left(\frac{\Gamma_{i}}{2} -i\omega \right)b_{s}^{\text{in}}\left(\omega\right)
$$
Neglecting $\kappa_{1}^{2}$ compared to $\kappa_{1}$ (I suspect this is related to the "small gain" assumption discussed in the paper, and since $\kappa_{1} \propto E_{p}$ this may be how this can be justified).
$$
\left(\left(\frac{\Gamma_{s}}{2}-i\omega \right)\left(\frac{\Gamma_{i}}{2} -i\omega \right)\right) b_{s}\left(\omega\right)=-i\kappa_{1}\left(\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(\omega\right)\right)+\sqrt{\gamma_{s}}\left(\frac{\Gamma_{i}}{2} -i\omega \right)b_{s}^{\text{in}}\left(\omega\right)
$$
$$
b_{s}\left(\omega\right)=\frac{-i\kappa_{1}\left(\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(\omega\right)\right)+\sqrt{\gamma_{s}}\left(\frac{\Gamma_{i}}{2} -i\omega \right)b_{s}^{\text{in}}\left(\omega\right)}{\left(\frac{\Gamma_{s}}{2}-i\omega \right)\left(\frac{\Gamma_{i}}{2} -i\omega \right) }
$$
Now, referring to the equations for the output fields
$$
\begin{align}
b_{s}^{\text{out}}\left(t\right) & =\sqrt{\gamma_{s}}b_{s}\left(t\right)-b_{s}^{\text{in}}\left(t\right) \\
b_{i}^{\text{out}\dagger}\left(t\right) & =\sqrt{\gamma_{i}}b_{i}^{\dagger}\left(t\right)-b_{i}^{\text{in}\dagger}\left(t\right)
\end{align}
$$
and taking the Fourier transform one obtains
$$
\begin{align}
b_{s}^{\text{out}}\left(\omega\right) & =\sqrt{\gamma_{s}}b_{s}\left(\omega\right)-b_{s}^{\text{in}}\left(\omega\right) \\
b_{i}^{\text{out}\dagger}\left(\omega\right) & =\sqrt{\gamma_{i}}b_{i}^{\dagger}\left(\omega\right)-b_{i}^{\text{in}\dagger}\left(\omega\right)
\end{align}
$$
Now, taking the first equation and substituting for $b_{s}\left(\omega\right)$ from the earlier computations
$$
b_{s}^{\text{out}}\left(\omega\right) =\sqrt{\gamma_{s}}\left(\frac{-i\kappa_{1}\left(\sqrt{\gamma_{i}}b_{i}^{\text{in}\dagger}\left(\omega\right)\right)+\sqrt{\gamma_{s}}\left(\frac{\Gamma_{i}}{2} -i\omega \right)b_{s}^{\text{in}}\left(\omega\right)}{\left(\frac{\Gamma_{s}}{2}-i\omega \right)\left(\frac{\Gamma_{i}}{2} -i\omega \right) }\right)-b_{s}^{\text{in}}\left(\omega\right)
$$
$$
b_{s}^{\text{out}}\left(\omega\right) =\left(\frac{-i\kappa_{1}\left(\sqrt{\gamma_{i}\gamma_{s}}b_{i}^{\text{in}\dagger}\left(\omega\right)\right)+\gamma_{s}\left(\frac{\Gamma_{i}}{2} -i\omega \right)b_{s}^{\text{in}}\left(\omega\right)}{\left(\frac{\Gamma_{s}}{2}-i\omega \right)\left(\frac{\Gamma_{i}}{2} -i\omega \right) }\right)-b_{s}^{\text{in}}\left(\omega\right)
$$
$$
b_{s}^{\text{out}}\left(\omega\right)=\frac{-i\kappa_{1}\sqrt{\gamma_{i}\gamma_{s}}}{\left(\frac{\Gamma_{s}}{2}-i\omega \right)\left(\frac{\Gamma_{i}}{2} -i\omega \right)}b_{i}^{\text{in}\dagger}\left(\omega\right)+\frac{\gamma_{s}}{\frac{\Gamma_{s}}{2}-i\omega}b_{s}^{\text{in}}\left(\omega\right)-b_{s}^{\text{in}}\left(\omega\right)
$$
$$
b_{s}^{\text{out}}\left(\omega\right)=\frac{-i\kappa_{1}\sqrt{\gamma_{i}\gamma_{s}}}{\left(\frac{\Gamma_{s}}{2}-i\omega \right)\left(\frac{\Gamma_{i}}{2} -i\omega \right)}b_{i}^{\text{in}\dagger}\left(\omega\right)+\left(\frac{\gamma_{s}}{\frac{\Gamma_{s}}{2}-i\omega}-1\right)b_{s}^{\text{in}}\left(\omega\right)
$$
$$
b_{s}^{\text{out}}\left(\omega\right)=\frac{-i\kappa_{1}\sqrt{\gamma_{i}\gamma_{s}}}{\left(\frac{\Gamma_{s}}{2}-i\omega \right)\left(\frac{\Gamma_{i}}{2} -i\omega \right)}b_{i}^{\text{in}\dagger}\left(\omega\right)+\left(\frac{\gamma_{s}-\frac{\Gamma_{s}}{2}+i\omega}{\frac{\Gamma_{s}}{2}-i\omega}\right)b_{s}^{\text{in}}\left(\omega\right)
$$
Lastly, I believe the conversion to the $a$ functions involves changing $\omega \rightarrow \omega - \Omega$ in the appropriate places.
Getting the second equation, $a_{i}^{\text{out}\dagger}$, should follow a similar approach.