Quite simply by not worrying about it. If a coin is profitable to mine then many regular miners will come and mine it, and so will botnets.

If a coin isn't profitable to mine, then it isn't worth it for botnets either, because they can either mine something else, or use their botnet for a less risky activity.

Who else is mining the coin really makes very little difference.

There is this myth that botnets are infinitely large and free to operate and therefore you can't compete with them, but that is really quite false. Botnets are a highly scarce and valuable commodity and they will only mine what is profitable to mine.

In the short term the most important thing to do is grow the coin so even a small botnet doesn't overwhelm the currently-tiny network. At sufficient size botnets don't matter.