A sad announcement for us fans! Another excellent batch of games goes by the wayside of history....
I think the decision to not continue the licence probably comes from both sides; to me, Fantasy Flight Games seems to have been moving in this direction for a while with the list of games and IPs they have. With Specialist Games returning and several solid electronic licences out there, perhaps GW also thought it was time to close a happy chapter and move on to new pastures?
Also, I think FFG making the announcement rather than GW is pretty normal; they're FFG products that are being discontinued, GW didn't have any hand in their production. It would be kind of nice to make some celebratory statement though, FFG has enriched the GW universe as much as it has enriched FFG!
The future shall be interesting: with IPs like Star Wars potentially getting table top game exposure from FFG, WH40K might no longer be the closest you can get to table top Star Wars miniature battles—without stable, competent support of the rest of the background by FFG, will GW and the 40K IP be able to survive? Maybe we'll be lucky, and GW will start doing things better again....
I've read @horizon's name in that Rogue Trader book, too! He's famous B-)
Sid Meier's Pirates always seemed like it could translate to 40K well... maybe it's time to actually play some RT RP!

Anyway, some food for thought,
Thinking Stone