[SPARK-12625][SPARKR][SQL] replace R usage of Spark SQL deprecated API

rxin davies shivaram
Took save mode from my PR #10480, and move everything to writer methods. This is related to PR #10559

- [x] it seems jsonRDD() is broken, need to investigate - this is not a public API though; will look into some more tonight. (fixed)

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #10584 from felixcheung/rremovedeprecated.