You really don't have to worry about botnets doing a 51%, there's not much profit in it. You'd be competing against other, "honest" botnets (weird thing to say) that are working for the coin, not against it.
Then I see no real problem. As long as they contribute to the network and behave themselves, all is well.
Sure, if you get an INSANE number of regular users to mine for themselves, then you won't have to worry about it. But most people are slow to adopt new things - and even less so when they don't see a clear benefit for them. "Who wants to make pennies a day for letting software run on your computer" - even if you could pay them in fiat, which most of them would be far more comfortable with - that's hardly a tantalizing headline. Most people would figure it's not worth the effort.
You can't assume the coin gets really big and also assume hardly anyone uses it. The idea of a wallet miner is that its very easy, probably a check box and a simple explanation ("Do you want to help secure the network, and be eligible to receive free coins?") at installation. Most causal users will check it and never turn it off (as long as it is well-written to stay out of their way, as we have both described).