Can anyone come up with a reason Schistosomiasis Control Initiative could possibly do more harm than good?

Did you read the link in the original post? The charity is not terribly transparent. Yes, it probably is doing net good, but there are other charities we can be more sure of that. Unless you have reason to believe that schistosomiasis is much more cost-effective to treat than other diseases, it is probably best to go with ones transparent charities with cost-effective treatments for other diseases.