I'd suggest you don't start with a Freedom of Information Act request. I'd do some research first and then do a FOIA request. In Virginia the request does not need to be in writing (can be verbal or by e-mail) but I'd urge you to put it in writing and to be as specific as you can. The reason for the research is so you can be specific.
I'd start by asking for (and it too is almost certainly public information) a copy of their NPDES (National Pollution Discharge Elimination System) permit. There should be a copy in the files of the local DNR office and you should be able to walk in and get a copy. It may run from five pages to over 100 pages but my guess is it will be between 10 and 25 pages. Pay for a photo copy if you have to and take it home and read it. Ponder what to ask for next based on what you read.
There should be some sort of Environmental Impact Assessment likely done by the cheese factory or their consultant. It may be referenced in the permit. There should be an evaluation of the dilution that is expected to occur and the ability of the stream to recover from the discharge. You never said what the five day BOD was that DNR permitted. If it's less than 30 mg/l (even with frequent modest violations) odds are you wouldn't see an impact (though there would be one) unless there is something else in the discharge. I've seen some astronomical permit limits (in the high hundreds) in Virginia associated with shellfish processing plants. If you see really high limits you're going to need some high powered help to get them reduced. See what you can find out about their flow limits and how many gallons per day they are discharging. Are they keeping within their limits or not?
There isn't enough information to say what's causing the effects you're seeing but one thing that you need to consider as a likely cause are nutrients. Pay attention to the nitrogen and phosphorus limits in the permit. TSS (total suspended solids) might be an issue, too and of course BOD. I'd also look to see what the permitted and actual pH is being discharged and if by chance there's any requirement for a chlorine residual (usually this is associated with sewage treatment discharges). Unless there's effective dechlorination the fishery will go to h*ll in a hand basket because it'll kill off the fry.
I'd call your regional EPA office - not sure which region your in but I'd talk to those folks. My experience has been there's a lot of bureaucracy in the EPA but there's a core of really dedicated folks too that like to find and fix problems. Look and keep looking for the right people.
I'm inclined to think the facts are on your side and the neat thing is you can get the facts on your own. It takes work but the only way to win this sort of battle is with the facts. Document EVERYTHING you do. Keep a phone log of every call - date, time, who you talked to and what you discussed. Keep copies (hard copies and electronic ones) of everything you do (e-mail and snail mail). Photograph your creek and keep records of what you photographed, what you saw - times and dates. Any stream data you can collect should be recorded too - biological, chemical and physical data.
This is pretty general advice but having been on the government side of the case for 33 years I can tell you, people that did what I described above and were persistent, tended to have better outcomes than folks who a more lax approach - even if they were politically connected. And that's something to consider. Your elected officials are there to serve you and if your DNR isn't serving you then by all means your state legislator should be given the facts.
I hope that's helpful for starters.