I don't see something in the code, that could make your readings noisy.
Are you sure source impedances aren't too high?
Few notes regarding how are you using SCF flag:
1) Since you are using AFFC=1 mode, you shouldn't try to clear SCF flag writing something to SCF. You should read any ATD data register to clear it in AFFC=1 mode.
2) Writing 0 to SCF doesn't make any sense. Doing it this way
ATDSTAT0_SCF =0;
is potentially harmful. In AFFC=0 mode it wouldn't clear SCF, but would clear EROTF and FIFOR flags. Proper code to clear SCF in AFFC=0 mode is this
ATDSTAT0 = ATDSTAT_SCF_MASK;
3) Since you have SCAN=1 and MULT=1, you should wait for SCF only once per loop. After SCF becomes 1, you can read both channels data registers.