@orthaic,
Thanks for asking. No, here are the facts as I understand them, taken mostly from media sources. Marques was basically the same sort of guy as Snowden, Manning, or Assange. He's an advocate of free speech, and government accountability. In much the same way that the aforementioned people are controversial, Marques was controversial as well. He was running a web site that basically used some space-age encryption technology to provide free web hosting to anyone, regardless of content, in a way that no one was able to find it, not even the NSA.
Frankly, I had no idea that my email was being hosted on his (Freedom Hosting) servers. As far as I know some other nerd was running the email software.
One day, a US government agency, probably the FBI, figured out how to hack his server, thereby locating it. Thereby locating him. They got in touch with Irish government, and worked out a deal to get access to the server. Somebody (possibly the FBI) then used the server to attempt to load viruses onto people's computer. Those are the known facts.
The rest is speculation. I feel I can safely speculate that the FBI were not after me. I'm a fat old man who spends about 80% of his time these days on video games. Most likely they were after drug dealers. While I'm not really puritanical about those sorts of things, I certainly won't shed any tears if the FBI arrests a bunch of drug dealers.
What makes the entire story interesting, perhaps controversial, is not that the people responsible (the FBI?) were hacking computers to get at evidence. They've been doing that for years, and I haven't anything bad to say about the practice.
What makes the story controversial is that they were so willing to hack hundreds (thousands?) of civilians in the process (like myself, heh). I'll stop short of complaining. I just think it's odd.
I think you might be confusing Lavabit with Tormail. I've never used Lavabit. Lavabit was the one that was (voluntarily) shut down because the guys running it didn't feel like helping the government help Snowden's email. I don't really believe that the two cases are related, although there are various conspiracy theories circulating.
Marques didn't voluntarily shut down his service. The first he probably knew about anything was when he was slapped in handcuffs. For what it's worth, I don't think he's as bad as people are making him out to be.
But I don't want to endorse his actions. If I were running a web server, I personally wouldn't allow unlimited free speech. I would probably ban pornography, for example. I don't really have anything against pornography, I just think it's important to have standards.