I can only speak for myself, but I'm totally disinterested in this idea. The issues talked about in this thread have absolutely nothing to do with USB Port related security concerns. GateKeeper and the quarantine system are a mechanism to constrain the spread of spyware and some types of worms. They have nothing to do with sandboxing apps to limit their access to physical hardware.
So far as I'm concerned, the problem here is not that the arduino software hasn't been designed explicitly to wiggle it's way through any tiny gaps left in educational computer deployments, it's that these computers have been setup to explicitly refuse students and access to these sorts of technologies. It's a policy problem, not a software bug.
Again, the specific issue here is that the Mac release of Digispark Arduino app is corrupt in a way which only affects users who leave gatekeeper enabled. Once this corruption is fixed, there will be no more issue, and the digispark arduino app will be as easy or difficult for students to run on their computers as any other app they downloaded from the internet.
You might be interested in the Digispark Xcode integration mentioned elsewhere on this forum. I would personally abandon the platform if Eclipse became the primary development tool of Arduino. The point is to have fun making silly little things, not to endure a bunch of training to learn how to use a ton of really complicated IDE software. Arduino is for people who aren't programmers, so they can poke together some bits and pieces and make a program and then get straight back to doing what they actually care about. These people are interactive multimedium artists, musicians, home automators, kids making silly robots, game designers prototyping new kinds of controllers, disabled folk creating their own custom input devices, gamers hacking USB connectors in their favourite oldschool gamepads, fashion designers making garments that glow, bicyclists making LED lights that flash better and keep them safer, and a million other things I haven't thought of yet. These people are magicians, here for the power of magic, not the craft of it. I am one of these people - my skill in programming comes from not having anyone else to solve problems I needed solved to create the art I wanted. My open source projects are to enable these creative types to get in and get out as quick as possible so they can spend time doing what they love, not learning complex computer systems. One of arduino's greatest assets is that their software has only six buttons, and all of them are useful and straight forward.
It is a grave mistake for a computer scientist to believe that anyone or everyone could intrinsically enjoy programming, and would want to learn more about it purely for the passion of programming itself. I hate it. I've been hating programming for over a decade! Programmers don't need yet another platform pandering to their comforts. Artists and experimenters appreciate Arduino. We don't have many things designed for us, and you can't take this away from us. It's ours.
And as a sidenote, I didn't mention enterprise deployments at all because that makes no sense. Arduino has absolutely no connection to "the enterprise", nor should it. The enterprise is boring and wasting time supporting it is counter to the goals of creating the best tools to support installation artists, and the enterprise can afford fancy expensive programming tools and can afford to pay people who intrinsically enjoy programming and designing embedded systems, so the enterprise can keep doing it's thing and leave our art tools alone.
* I'm just an individual visual artist, I'm not digistump staff and my views do not in any way represent theirs. I am also not a member of the Arduino group, but I have contributed to some open source software used by the digispark project *
All that said, this has been a very negative post. I like education a lot and I'd love to see digisparks used more in education. All students should have some basic fundimental programming skills and understanding. It's very empowering to be able to mess with computer systems and make them dance for you.

If I can help make the digispark more useful for educating kids (for fun!) I'd be interested. A friend and I were playing with some visual programming metaphors a little while back for making tiny robots using digispark-compatibles and experimenting with their little AI brains. There's some interesting stuff to be done there!