Hmm...interesting idea. And a big one; coding projects like this are complicated and error prone. You thought seg-faults were bad? Trying tracking these kind of seg-faults. Sounds like a nightmare, but obviously people have done similar.
One thing that helps is Toady appears to be a reasonably accomplished programmer; the kind of changes that pop up on the dev log with regularity imply he has structured his code rather well, which I would assume might make a code injection easier, but by no means simple.
A second process would be much easier to handle, and since much of the research into the structure of DF memory, it may even be pretty straight forward to reverse engineer the map. But here is the problem:
It is glutted, bloated, inelegant, and hackish. Granted, the very nature of Modding, especially in the good-ol' days, is cracking the game code. How easy the developer makes this is up to them, and the mere fact that there is enough nerdom on this forum alone to allow things like Dwarf Manager and 3Dwarf to even exist is a testament to both Toady and the community.
But an exterior program spying on the DF memory so it can render a "nicer" 3D or psuedo 3D GUI in real time I don't think helps the game itself much. Yes, it is cool. Yes I use 3Dwarf, yes I speak the graces of an ASCII art GUI while at the same time grinding away at graphics sets and tilesets to make the GUI look "nice," but that is because I am a geek. At the end of the day, it is just a PSD file, just an image that uses what the game already has and does. Building a huge thing that augments the GUI by spying on the original is cool, but not necessary. A better investment of our time would be to develop a document specifying what the 3D interface should be, after much discussion and work, and even some prototyping. The major hurdle in any GUI design is the design phase and the research that goes into it, something that Toady can not do on his own because he simply doesn't have the man power.
We get away with an all-keyboard interface because that makes sense to us, and the affordances we make as geeks make it okay that the hot key for a floodgate can be any of three different keys. I think we can safely assume that a great majority of the DF community is used to command-line OS control and programming, including HTML. This level of arcanity (hah, that should totally be a word) is okay because we are in the trenches dealing with it anyway. Furthermore, a single developer for a game as complex as DF is not exactly the best person to design a GUI, because he is in the middle of it. But he is the best person to implement it, especially since this is Toady's livelihood..
So my opinion is that any work in this area should be at least a thought experiment, at most an organized, concerted effort to figure out how the hell one would actually go about controlling a game that seems to be so well suited to 2d layers and not isometric slices. That way the Bay12 Team has a good starting place at worst, a detailed design document at best.