We are concerned about splash back and aeration of contaminates from the drain. No options on moving the equipment due to lack of space so we would have to create a system to off set the run off from the machine or create covers for drain to minimize the aeration and splash back. We are concerned about SQF auditing because this will be our first year so we are trouble shooting issues such as this.
I don't have direct experience of SQF but when auditing factories, this kind of practical oddity is one of the first kind of visual items I would be looking into.
The problem is that IMO it goes against basic hygiene logic so you will need a strong validation to justify its acceptance.
You will see other threads here regarding the minimum floor clearance for machinery using exposed products. This is just for a random floor surface. Now add a semi-open drain and you can see the risk go ^^^.
Simon's suggestion is what many factories do since at least it "looks" not unreasonable. But depending on the location, some heavy duty, non rustable, "panes" may be involved. The first objectants are usually the clean-up crew.