There is a limited number of passes leading into the coastal ranges from the desert. The most cyclist-friendly route is IMHO the one from Borrego Springs to Ranchita.
Well, if you don't mind one hill. That hill climbs 11 miles from Borrego Springs Christmas Circle at 600' to the summit at 4227' just east of Ranchita. There's no shoulder, and parts of it reach 8% grade, but traffic is usually not too bad.
http://www.youtube.com/watch?v=euHdevqgZVE
A longer alternative is to head south out of Borrego Springs over Yaqui Pass, up to Banner at 3000', then up the Banner Pass Rd (Hwy 78) to Julian at 4200'. Longer, but the climbing is broken up into sections, and Julian is a nice tourist trap (whoops, I mean town). From there, you can descend east and rejoin highway 79. Shortly before Banner, San Felipe Road does climb NW up to Ranchita on a gentler grade, if you do want to head that direction.