It only disables them for the rest of the current session, as far as I'm aware; then again, I've failed to register a single achievement, so perhaps not. Seems a bit silly that it blocks them when it's a single-user game, though: perhaps that's something else that needs looking at.
I just think they went a little over the top with it - I'm not sure why they couldn't simply disable achievements only if certain commands were used - for example basic functions like saving games and the inevitable FIXME commands being safe from that.
As for the UI, well I've given in for the minute and bought a 360 controller wireless receiver, just to see if it's any more bearable. On the plus side I've got The Last Remnant here which, although it runs about a million times smoother on PC and looks class, is clearly only playable with a controller. I don't even think it HAS mouse support haha.
On a side note, does anyone know if the 360 pad keyboard works with hotkeys? It would be nice if you could still map 1-8 on your attachable pad keyboard. I'm not getting my hopes up mind.