To be honest the Botnet thing is one of Monero's dirtiest secrets. It's a shame there is no way to avoid it yet. It is a stain on the whole project IMHO. But there are worse things.
I honestly don't think it's that bad. If/when Monero becomes more popular and easy background mining is implemented in the core wallet/daemon, then it will be much less of an issue, but even at the current levels of popularity and usage I don't think it's such a big deal. Would you rather have shady botnet operators collecting 10-80% of coinbases, or would you rather have shady operators like KnC, Butterfly Labs, Gaw Miners, etc. collecting a significant fraction of coins? It's a tradeoff, for sure, but one that I don't think is necessarily a negative compared to ASiC-only coins, leaving aside GPU-only coins.