The problem description doesn't explain what the actual problem is.
OP said that the connections are between the mining pool server and bitcoind. I suppose the rpc port of bitcoind isn't exposed to the internet, therefore can't be flooded. Also, most of the time it makes no sense to leave it open for anyone.
Ahh, okay. So forget the DDoS resistance stuff. But we still don't know why this is a problem.
If all the pool server needs is the 'getwork' output, it seems like a much better solution is to avoid polling altogether and have 'bitcoind' put this information in a file or write it continuously to a queue or something. (Assuming I'm understanding the problem correctly. I'm not 100% sure that I am.)