[Anaraxes]

Square megahexes don't solve the problem of having half-a-hex. (Or square, as the case may be.)

There's no need for a penalty for half hexes. If there's at least half a hex on your side of the wall, use it like normal. You're not pretending rectangular rooms don't exist; you're pretending that the hexes don't. (The D&D square version is realizing you don't have to pretend that all buildings are exact multiples of 5 feet in each direction, as well as always having walls aligned exactly parallel with the compass directions.) It's just a mapping convention, and there's always some granularity to cope with.