One possibility is Microsoft Windows malware that targets existing Bitcoin miners and steals a portion of their winning blocks. The impact would be.
It's impossible unless this malware also provides all those miners with work too.
If the malware also provides work effectively stealing a portion of the hash rate it would still have the impact I mentioned.
Couldn't it just intercept golden nonces and discard them? That would cause bad luck, with the same/high hashrate.
When mining, you are doing a brute force hashing of everything that will go into a block. The merkle tree you are hashing includes the address that a block will pay out to if it is found, along with a "coinbase", which is per-worker information added by the pool to make a miner's work unique. You are also hashing all the transactions to be included in the block. Mystery miner's blocks have zero transactions, they are different than a normal pool's blocks.
Because of the pool-specific and worker-specific data included in a block, you cannot simply pick out certain hashes like one that solves a block and send them somewhere else, they would still pay to the original wallet's address as that information is embedded in what is being hashed. If the miners were getting altered work, they could not send it back to the original pool as the shares would be invalid, they would not be hashes of what the pool was requesting.
In order to steal work, the attacker would have to pWN the pool. If you can get into deepbit and silently get 10% of their block finds to pay to your wallet, that's better than just stealing their wallet once. As about half the pools here have been compromised at some point, we see that getting in is possible, but rootkitting and altering pool software to make a continuous undetectable diversion of mining rewards would be more difficult.
If it's a botnet then this could potentially mean trouble for it in long run
A yet-undetected botnet seems difficult to believe, it would be on the scale of Zeus2. I have seen no bitcoin bot alerts since Sept 2011 and those were naive trojans. CPU mining my Core 2 Quad (probably faster than the average internet-connected computer) gets 11mhash/s; to get into the 2000ghash/s the miner is likely doing, they would need 200,000 such fulltime botty machines. A CPU+GPU bot would need fewer, but I have a feeling that systems with GPUs running mining-capable drivers that can hash faster than their CPU are in the minority, if we were to survey all Internet-connected machines worldwide.