Hi. I have completed fallout 3 with good karma to level 30. And now I want to do level 30 with bad karma. Can my good karma still save if I do a new game? Thanks!

Yes, just don't delete it or save over it.

Click new game, and save in a different ("create new slot" option.) The only save file that will be overwritten is the Autosave slot.

Also, in case you missed out, if you click into the main menu, there is an option to "save" your game - autosave is not the only choice.