Well subsequnet culture would be needed to tell if it was for sure hoof rot or not, but it sure sounds like it to me. Foot (Hoof) rot is caused by synergistic relationship of two different bacterias. Bacteria known as Bacteroides nodosus occurs naturally on the hooves of deer and bacteria known as Fusobacterium necrophorum is naturally occuring in fecal matter. F. necrophorum does not penetrate healthy hooves - the problem arises when there is an abraison in the hoof wall or foot already. In cases where we have deer in pens (congregated) both bacilli have higher populations in soil and fecal matter. Foot abcesses may be caused by B. nodosus alone, however true foot rot disease is caused from both of these bacteria. Moist soil conditions contribute to the spread of the bacteria, but I often see cases and it is well documented that this disease is very prevalent in dryer years when deer congreagte around water sources. In the past Gentamycin has worked, Gentamycin kills the B. nodosus - which in turn takes it out of the equation and eliminates the synergistic effect. Vaccination programs are the best preventtative medicine for this, I use Fusoguard. I would get with your vet and start a program and treat your deer - quickly.
Also for treatment of this disease in sheep, it is recomended to trim the hoof wall to the quick and soak infected hooves for five minutes in a foot bath contaning 90% water and 10% formalin (37% formaldehyde) or 10% zinc sulfate. I would use zinc sulfate because it is essentially as effective and safer to handle. Many sheep operators isolate limpers and repeat the process one week later, then turn into uncontaminated area.
I would treat, isolate the limpers and rest the pen. Treated deer can theoretically infect other deer, just a word of warning. This disease can be a headache, good luck and I would get with your vet - treat your deer and vacinate others, if this is what your vet thinks you do indeed have. I have seen several other documented cases up north and a good friend of mine has had it in his pens, so thats why I definately would not rule it out.