One way to get around this is to use Calculated Column with formatting rule for the Body column. My suggestion is to use the formmating runction TRIM for the Calculated column on Body column. White space including new line character can be removed allowing the CAML filter to check on the Calculated column.
1. Create a Calculated Column "Body2" with formmatting: =TRIM([Body])
2. Use CAML Filter on Calcualted Column
Let me know if this helps.