There is not really a ghetto in the same sense as big cities have. There are socio-economic conditions that cause more crime. Do not use Craigslilst, too many scams. You contact a real estate agency or property management company that has rental listings. Dont look online for these strange sites you mentioned. For Rent.com or Apartments.com are legitimate but a personal approach will get what you want.
You should come here and live in a residentail hotel for a few weeks and talk to other people to find out where you should live. For $1200 in San Francisco you may find a basement apartment away the historic and tourist neighborhoods in plain vanilla residential areas like Outer Sunset, Outer Richmond, Panhandle, Pt Lobos, Western Addition, Cole Valley, Excelsior, Outer Mission. Do not look at Bayview, Hunters Pt, Visitacion Valley, Junipero Serra, Bayshore, Civic Center, Tenderloin. Do not look at Oakland, Richmond, Vallejo, Berkeley because you dont know what neighborhoods to avoid.
Housing prices are starting to go up again. I would suggest to you the Peninsula, south of San Francisco and places like Brisbane, San Bruno, Daly City, San Mateo, South San Francisco and you can take Cal Train to work. In the E. Bay where the BART runs, you can check out Hayward, San Lorenzo, San Leandro, Fremont suburbs.
You might want to look at Novato in Marin county but it will take 1 hour ride to S.F. because there is only a commuter bus and no trains. You can find a 1-bdrm. for $1200.