Yeah, some time down the line we will need to update the sidebar menu. As you said, make the map omnipresent and perhaps move the various tabs down to the build menu. The build menu takes up too much real-estate in the side bar at the moment.
Having the map rotated 45 degrees, just like the isometric map itself, is the eventual plan. However, this big UI update is a few more updates away. We're currently just using default UI elements as much as possible in order to save time and make the rest of the game more functional first.