If you can get that duck poop before it gets to the culvert, do it. This might be a good place to put in a small garden pond and grow duckweed, cattails and arrowhead (all three are easy and, soak up lots of nitrogen, and your ducks will love them). If that's not doable, then the idea of catching it after the first culvert before it flows out to the larger wetland is probably best. I also like the idea of making the straight ditch more of a meandering stream. However, if you can get rid of the ditch entirely, replacing it with a series of swales, that'd probably be ideal and the most healthy solution for protecting the wetland downstream.
The way I see it, the dept of making you sad is always going to be a threat, no matter what you do, unless you seek them out and have them dictate to you what you should do. This is even if your solution would work 100 times better than theirs.
And even then, they might still come back in 10 years and say that the person who told you to do X was wrong, you shouldn't have listened to them and it's now your responsibility to do Y instead (and pay them fines with money you don't have, of course).
The best thing is to do everything you can to ensure that they NEVER have reason to visit

If they do anyway, try to make it so they never have reason to look closely. If it looks healthy and natural, and water quality is better than average, there should be no red flags thrown.
I'm no expert, but from where I sit, your current plans look to be on the right track

Just be really careful when stirring up sediment and muddying those waters. Try to go easy with it especially when expecting heavy rains.