Hello Johannes,
There are a few paths forward. You can use simulation states to start the model in steady state: https://www.mathworks.com/help/simulink/ug/saving-and-restoring-simulation-operating-point.html
Alternatively, if you do your frequency sweep in post processing, you can just delete the first ms without modifying your simulation.
You can also use the frequency sweep tool in the controls sytem toolbox, and specify how many cycles you want to give the system to reach steady state before doing the frequency analysis: https://www.mathworks.com/videos/frequency-response-estimation-68884.html?s_tid=srchtitle
Regards,
Joel