Botnet wranglers have an advantage over "normal" miners, and if they're not a dominant fraction of the mining that's happening, they should be able to mine with a comfortable profit while everyone else's net profit is driven to (close to) zero.
As I've said before, from the point of view of the coin network, botnets are just another form of mining rig. Assuming what you wrote above is true (though it is harder to understand the botnet owner's cost structure as you point out), this is not very different from someone mining with a 0.5 W/GH ASIC while someone else is still mining with older 1 W/GH ASICs. Obviously the guy with the 0.5 W/H has a higher profit margin, and the guy with the worst efficiency is barely breaking even.
It is most certainly different to the computer owner, but I've also said before that botnet mining is very likely less socially harmful than other uses of botnets (spam, DDOS, etc.) because the costs are borne by the computer owner who is in the best position to either prevent it or address it.
EDIT: One last point. Probably the best way to detect a mining botnet on your computer is to mine with it. If your hash rate drops then you know something is wrong, be it hardware failure, software failure, or a botnet. There is no way for a botnet owner to steal your hash rate without reducing your hash rate.