Publishers are cracking down on the free to read sites, not the scanlators. Sites like MangaFox and OneManga are high priority for them. When Scanlations first took off publishers watched carefully to see how much it was going to hurt sales. Turns out scanlations helped. Some people would download and read the manga on their computers, talk about it with their friends and get them excited, then they'd go buy the manga when it released here.
When the free to read sites started showing up the effect was the opposite. Now the people who refused to download the manga for various reasons(most are just too scared of viruses to risk it) could to go to a safe site and read the manga without having to download it. The other reason they're cracking down on the free to read sites is because unlike (most)scanlators, mangafox and onemanga make money every time you visit. The sites host ads people pay to have displayed there, making them money off of work other people did.
I had heard about the publishers crack down on these sites a couple months ago and honestly, I was hoping MangaFox would be the first to go. The mods and admins there pissed me off. First they used ads that had sound clips (2 per page) that were really annoying, would overlap, and just make it hard to concentrate on what you were trying to read. Second they used a program by google for their ads and when someone brought to attention the mature content the ads were placed with to the companies the ads were promoting MangaFox quickly got rid of most of their mature content. Now I wouldn't have been pissed by this if it had been for any other reason than the fact that google was going to pull to their services and thus MangaFox lose it's ads and money.
Anyways, long story short, scanlators are safe by my understanding. It's just the free to read sites we'll see disappearing.