I can get why GW went after Vassal40K. They aren't sitting on a rock solid IP to begin with. Lets face it, Orks, space marines, elves, bug hordes, etc. aren't exactly groundbreaking shit. They've got their own style on it all but in the end it's a lot of stuff that's not a long way from things considered public domain. As such GW has to aggressively defend their IP. You see part of IP rights is that you have to defend them. If you don't then they can become public domain. Kleenex, Band-Aid, etc have all fallen prey to this. In GW's own arena Tolkien's estate lost "Orc"s because they didn't defend it for quite a long time and as such many people had started to use it. The judge in their case decided that orcs was now public domain and that was the end of the Tolkien's estate claim to IP over orcs. Given how shaky GW's foundation is with what they've got they can't let even a small chink into the armor. They're one judge's ruling away from losing their IP.
They've also got a lucrative license agreement going on for their computer games. They might have verbiage in their license agreement that requires them to squash anything like Vassal40K. It could also just be them protecting a revenue stream. The license agreement is only worth something if it grants exclusive rights. Something like Vassal40K could infringe on what a potential licensee wants to do later on down the line and with a free program already in the market the licensee might chose not to purse it because of that.
Now ultimately I think GW's problem is that it's mantra has long been, "We're a minis company." They're obsessed with selling minis. They will stomp on any idea that could result in fewer mini sales even though it might increase total revenue for the company. It's a very odd stance. They need to take a holistic approach and look at their company as promoting WH40K in whatever form it takes. For instance realize that the rulebook and codex drives mini-sales and the slow pace of updating codices can slow sales of certain mini lines, eg Necron, Dark Eldar, Inquisition, etc. Their books and background are every bit as important as the minis. For instance there are a lot of people who don't give a shit about the game but love the setting. In the video games aspect Vassal is a great example. Why not go to Relic and show them Vassal40K? Have them make an official version, even bring in the guy who made the module originally, and make a version to sell commercially? Because it might hurt mini-sales. Never mind that they'd likely sell a copy of it to every WH40K player and a ton of fluff lovers as well.
GW needs to pull its head out of its ass in general.