They made implications that he survived though haven't actually confirmed anything.
Purefoy (joe) said at comic-con “It’s a phoenix risen from the ashes.” in regards to his character.
The writer would neither confirm nor deny anything.
They never really confirmed his death on the show either, they found remains and dental/dna said it was joe but given how extensive his network is, that's easy to forge.
There's also that guy joe killed at the end, that body has a purpose and I think it's this.
Plus he's signed on as a "regular" for season 2. While that could mean flashbacks, it could also mean he survived.
http://tvline.com/2013/07/19/james-purefoy-returning-the-following-season-2-comic-con-2013/Seriously this pos is getting a season 2? Why not just end it with everyone dead, would have been good for a poe based show.