I have the same problem. I had to import a 22MB csv file into tilemill and got the same error.
Although I don't have a working answer for you, but I would think either:
- Convert csv to SQLite export files http://www.mapbox.com/tilemill/docs/tutorials/sqlite-work/
- Configure the buffer for tilemill (however I doubt this would be the best because my tilemill cant take 5 GB of memory when doing points/markers rendering, increasing the buffer would make things worse)
I will keep experimenting with the ideas, and update this thread as soon as I found something. Also, I am looking forward to the tillmill pros out here for the best working answer~!
Best