After posting about this on the EEVBlog forum, I was pointed to a particularly neat chip for DC-DC conversion... The MC34063. It can do boost, buck or inverting conversions, and has a very wide voltage range. The next versions of the Hydra are going to be made with two of these - one to generate 5V@500mA and the other to generate -12v@50mA. J1772 pilot generation isn't so fussy that it requires perfectly balanced supplies or anything like that, so I'll just use the incoming +12 rail for the "high side" of the pilot square wave and the converted -12 volt supply for the "low side." With the Sziklai pair architecture (4 transistors per car) and the DC-DC converters, the BOM price for a Hydra board has probably dropped by almost $10.
I'm waiting for some of the new parts to come in the mail to verify the board footprints before ordering the next board version.