This is always more a question for the performing artists themselves. As an engineer, the more channels you can have, the more flexible your life will be. For a newer engineer, it might cause issues if they aren't familiar with complex mixes of orchestral music, but if you have a solid engineer, it will be far easier for them to work with independently controllable channels for each section.
The biggest reason not to do this is that it impacts the way the orchestra plays and can potentially take longer to record. Instruments in an orchestra don't just play by themselves. They are part of a larger whole. They depend on each other to feel the music and contribute to it. With a full orchestra recording, you have more people who could make an error requiring another take, but they are all playing together so it can theoretically take fewer passes.
When recording individual sections, you will want to first record the entire orchestra in a rough capture that you can then use as playback to the headphones for all the musicians to play along with. This will prevent the individual pieces from not lining up, but still is slightly more complicated as they will hear themselves playing twice.
You could further get around this by doing a rough recording of each individual section and then recording each section listening to all sections but their own, but this takes even more time to get done.
It's also a bit of a different experience playing to a recording than it is playing with other musicians live as you lose the back and forth dynamic where they can respond to each other. If the orchestra is more jazzy, this can be a particular challenge, but really depends on their preferences balanced against your own needs for flexibility in the mix.
If the orchestra themselves is suggesting it, they are likely comfortable with the approach and can help out with what processes have worked well for them in the past. The main concern then would simply be that your mix engineer is experienced enough to do a proper mixdown of an orchestra broken up by sections.