Since v1.4, Content Elements is compatible with SafeCracker. The only limitation are that the Gallery element in Content Elements is not supported via SafeCracker and additionally, Rich text acts as a simple text area field.
To make the Content Elements work with SafeCracker, you need to include jQuery using the include_jquery parameter as shown in the example below:
{exp:safecracker channel="test_channel_ce" include_jquery="yes"}
<!-- Required title field -->
<input type="text" name="title" value="" />
<!-- Content elements -->
{field:content_elements}
<!-- Submit button -->
<input type="submit" name="Submit" value="Submit" />
{/exp:safecracker}