One problem with third-party user interfaces is that damn near everyone would wind up using them. Even if a decent API is used, things would break between versions, leading to (sometimes large) gaps in time between a new version of DF being released and the third-party UIs catching up.
This is very annoying for the community, at least.
Consider the current situation with tilesets, Dwarf Therapist, Reveal, and so on. For a surprisingly long time after the release of 0.31.01, people were flooding the IRC channel fairly regularly with questions about whether or not this-or-that tileset still worked, if there was a Mayday pack out yet, if Dwarf Therapist worked for it yet, and claiming that they wouldn't even play the game until there was.
In other words, there's some inherent instability in having people rely on third-party software that needs to be updated regularly. It winds up being frustrating for the players, and frustrating for the community in general.
To that end, I think the best solution is for the game itself to have a decent user interface at some point. I agree that the new military controls are the straw lead weight breaking the camel's back at the moment. I don't think a perfectly sustainable long-term solution is necessarily the best or most urgent thing to do right now, but things need to be workable and remain that way.