Interesting. As far as I can see, there is no prohibition here. As long as the account is of a type that is allowed to receive ACH entries (i.e. it is a DDA or savings account), then the item can be posted. Under some cases, ACH items can be returned as an R20 for Non-Transaction Account (such accounts being subject to Reg D limitations, for instance, or falling outside of the allowable types, such as a brokerage account), but as long as the account in question here is just a bland business checking account, I don't see that there would be any problem in posting the item.
As to the advisability of one of the LLC partners doing this, I cannot say, but that's their decision to make. At a very broad level, the RDFI simply automatically posts whatever is sent to it as long as the necessary criteria are met, and usually the bank really has no idea of what items are coming in and therefore generally doesn't worry about the fine nuances of cases like this.
But I'm not an LLC expert and perhaps there is indeed some legal prohibition here that would trump NACHA rules. Anyone?