The science of gene therapy already exists, however in practice it is pretty much not a major target of pharmaceutical companies due to massive complications in a majority of clinical trials thus far. A number of patients have died from complications related to gene therapies where good copies of a defective gene have been inserted using a few different vectors to deliver the gene. Basically unless the disease is already deadly I doubt it will be a target of gene therapy simply because the risks are too great for something that can be managed in other ways.
As far as the genetic markers go it will be used to diagnose crohns in a similar way as the breast cancer gene, Rb gene (retinoblastoma oncogene), and other similar genetic diseases are diagnosed. Basically they can use the specific markers to easily determine someones risk for crohns using a very simple panel of genetic analysis similar to when you karyotype a fetus in the womb if there is family history for a disease like Huntingtons.
The one good thing knowing the genetic markers is that there is a ton of other information that can be gleaned from the markers. An example would be to know which biological pathway the genes lie in and determining their exact function in the pathway. You can then selectively target parts of the pathway to restore or inhibit function as dictated by the product produced by the defective gene. Often knowing a protein target makes designing a drug a lot easier since finding compounds that bind tightly to a known protein is fairly simple. Its finding safe compounds that are also active that is the hard part after you find a number of hits to begin with.
Basically as you all said a genetic study to find genes linked to crohns would be a huge asset, but only a baby step toward any new treatment. The standard development cycle for a drug takes in the vicinity of 8-10 years from start to finish. If this study isn't complete, then basically we're at least 8-10 year away from even potentially seeing a drug related to these results unfortunately. On the other hand you have to remember there are drugs that are constantly nearing approval that blow anything we currently have out of the water (or at least in most cases this is the case). At some point a new drug will come out that makes a current treatment less toxic or that just completely changes the face of our treatment as has been seen with a number of other diseases. Obviously we can hope for something big out of this, but the reality is the world of pharma just doesn't move that fast.