Questions for discussion:
1) Should such research be even done? In civilian facilities? With a rather minimum security? What if some nutjobs broke in, stole samples of the virus, or the infected animals, and used it as a doomsday bio-weapon?
I would say a cautious yes. With any disease, one of the very first things to look at is "what mechanisms are feasible for that disease to use to become worse?" - often mechanisms by which they can become drug-resistant, deregulated in proliferation, etc. And the way to do that is by trying your hardest to actually make these super-diseases so you can find out the how, and then develop methods for stopping it when it happens out in the real world. That's really the most useful way of doing it, which is usually fine as long as it stays in a confined laboratory environment.
Making new viruses is a standard part of lab procedure in a lot of labs. Often they sound very scary. If you say "I've made a virus for a leading cancer-causing mutation and put it into the HIV virus shell", people go ballistic - realistically though, it's probably less dangerous than half the stuff you've got under your sink, because these things normally have built-in safeguards (knocking out a bit that makes the nastiness but isn't involved in the proliferation, for example). Is the one in the article similarly safeguarded? I don't know, and I don't know enough about the specific virus to know if that's even reasonable. I would hope that they would take every possible precaution to make a "safer" version (that proliferates the same but doesn't kill you, for example) before going further with it.
In addition, "civilian facilities" in this case would be the equivalent of Physical Containment Level 3 at the minimum or almost certainly Level 4 (that's the Australian system, but I'm sure the Netherlands has a roughly equivalent one); neither of these are your chemistry lab from undergrad. PC3 requires a very significant level of safeguard, and PC4 are extremely rare and very well-safeguarded facilities for serious stuff like dangerous infectious diseases (I think there's only one in Australia). It would be hard for something to get out of PC3 by accident, but probably easy enough by malice from an insider. If you just broke in and didn't know exactly what you were looking for and exactly where it was, we'd be talking real needle in a haystack stuff. PC4? Not so much, I don't think - that's a level that involves showering to go in and out, airlocks, bunnysuits etc (all the movie stuff), and you certainly wouldn't be able to easily smuggle a sample out, even as an insider.
2) If it's so easy to recombine influenza strains in order to create deadly forms of it, how come no terrorist group has done it yet? Are the jihadist too stupid to do this, or do they just need more time?
Making new viruses is potentially an easy, routine and run-of-the-mill part of normal laboratory procedure. If you have a lab and access to scientific facilities and supplies, no problem at all. But getting access to this stuff without the resources of the international scientific community? Not so much. There are so many things that you need, that you can't get access to if you're not a lab. Getting the DNA you need in the first place, in the form you need it, is going to be a massive challenge. Then plenty of very specialised reagents, and a lot of very specialised, very expensive equipment of the sort you can't just "acquire". And then of course you have to know what you're doing and spend years optimising etc, and overall it's not the sort of thing that's feasible from a cave in the mountains with a bunch of jihadis who, not to stereotype, seem to me not to usually be big on their medical science knowledge. It would really have to be an officially-sanctioned lab in a rogue nation, but even then the amount of stuff needed from elsewhere would very likely raise a lot of red flags.
3) Has this story been hyped (oh yes).
Of course, it's a science story in the media. Usually there's no more than a passing relationship with the actual truth. I'd be interested to find the actual paper though and see what the actual story is.
4) What preparations have you made, if any, to survive the inevitable "big" influenza pandemic that will kill hundreds of millions of people worldwide and bring our civilization near collapse? (loaded question, I know)
Years of training have meant that I can spend long periods of time playing games like civ on my own; maybe just sit it out until it all blows over?