The trick to building a lighthouse or any other semi-complicated building is to build it in a separate .vmf file and tweak it until its the way you like it, and only then copy it back into your map.
Basically I made an 8 sided arch with a wall-width of 8 for the outside of the lighthouse, and then moved all the verticies onto grid lines. Then I used the arch tool again to make a spiral staircase, and cut holes in the walls with the clip tool to make the windows. Be sure to only cut holes in the walls that are not angled, or else you are in for a world of hurt trying to get everything aligned in Hammre. The .vmf is here, you can take a look:
http://www3.hmc.edu/~nalger/dm_island17_vmf.zip
Everything to do with the lighthouse is in the "lighthouse" vis group, so I suggest you hide everything except the lighthouse and terrain vis groups so that the map doesn't lag your computer.