I would give it some time and keep up with the water quality, as I think it looks pretty good compared to what it looked like previously. Maybe also consider a different clown species that is a natural symbiont, such as saddleback's or sebae's, that may not be as "rough" with it (if the cinnamon's are indeed too much for it)?
I have tomato's (similar to cinnamon's) with my new gig carpet, which seems to be as large as your Haddon's, and they present no issues for it. Maybe your previous issues had nothing to do with the clowns, and the nem was ailing independent of their presence?