So even if legalising it would make those markets lose profits, they still have a lot of nasty things to sell -- so taking them down is still the best thing to do for the moment, IMHO.
Further, the costs of these LE operations is very high to catch some small fries. These are extremely counterproductive.
I think that's the point. As far as I understand their reasoning (although I don't agree with it), is that some people buy drugs when they are easily accessible over the internet, but wouldn't do so if they have to meet risky people in person AFK. Of course, people who want drugs will get drugs, somehow, and if it's safer, that'd be better. But they want people to move into the riskier meat-space as it's easier to keep track on people and eventually arrest them then.