Botnets are only a significant concern
while the mining usage is small.
And that applies whether your Pow is designed to be ASIC resistant or not. However it perhaps does beg for making the GPU at roughly power efficiency parity to the CPU.
As you mention in your subsequent post, algorithms that make use of recent CPU and OS features are likely to hinder botnets to a significant degree. This is already the case with Cryptonight. Older botnet computers are less likely to have AES-NI, more likely to be 32 bit, and more likely to have older, slower CPUs with fewer cores and/or less cache. Together these reduce the effectiveness of a botnet computer relative to an efficient CPU or GPU miner by perhaps a factor of 10. Exotic botnets (routers, etc.) will fair much worse.
Currently the Monero network consists of the hash rate equivalent of very roughly 100K modern desktop computers (64-bit, AES-NI, 8 MB cache) or mid range mining rig GPUs (750 Ti, etc.). For a botnet to 51% attack that would require roughly 1M of these more-likely-to-be-botted computers. That is certainly possible, but it is a obstacle. How many botnets are 1M+?
Smaller botnets that decide to honestly mine instead of attack increase the hash rate and help secure the network against attacks. They are a problem for the computer owner, but they help secure the coin just like any other miner. The more of these there are, the harder it is to ever attack the coin, even with a botnet. How many smaller botnets are there compared to 1M+ bot ones?