Hi Alexey,
thank you very much for your reply - i am curious to try out said script once it is available!

In the meantime, i tried Paulo's approach and got some interesting results.
From an existing Point Cloud, the workflow was like this:
1) Classify Ground Points via "Tools" --> "Point Cloud"
2) Classify Points via "Tools" --> "Point Cloud" (there does not seem to be an automatic function to classify points as water, so i did that manually with "Free-Form Selection" and "Assign class" in "Tools" --> "Point Cloud"
3) "Resize Region" to cover my sample
4) Build DEM from pointcloud with all points but water
The results are very promising and show a much smoother water surface, as the "Build DEM" command seems to interpolate all the missing parts on its own - no need to create a polygon which overlaps with the DEM on each side to get the heights.
The before image 1 (longitudinal) shows valleys and mountains on the water surface which differ up to 12 m, image 2 shows the lateral distribution of distortion. Interestingly, the overall water level in image 2 is pretty flat, even though it shows valleys and mountains. Image 3 shows the new water surface in longitudinal direction, image 4 the lateral water surface. In image 4, there seems to be quite an incline from the left bank to the right bank of about 0,5 m in water level, whereas the original (image 2) was kind of flat and more realistic when you ignore the distortion bumps.
So, to summarize my findings:
Generating a DEM from a classified Point Cloud without the water-class seems to be a feasible approach to my problem, even if it still requires to manually classify the waterbody.
Yet i am curious to see what Alexey and the Agisoft-Team come up with

Thank you all for your help!