Yes, disabling atomic save is totally safe.
Just to know, why hitting save in rapid succession? I mean, after the first hit the file is saved, and for sure is not modified if you re-hit ctrl+s...
I replied to another forum question where I answer this:
The point of quickly doing ctrl+s is just to show the bug in an easy way, at least for me. The error comes even without doing this, but less frequently. Also, I sometimes press the 's' too long, so I accidentally get this message.
Because of this bug, I have lost files, because the error occured when leaving sublime during a reboot