I think I remember replying to your email on this. But, I will leave the answer here as well :)
When you go to your Entire Collection tab, select all songs you want the cue points deleted for, right-click and select "Remove Cue Points". You will still see the cue points inside MIK, but they will be removed from the actual file. You may have to analyze your files again in your DJ software to detect the change.
If you want to disable the cue points from being exported in the future, just go to MIK Settings -> Export Cue Points -> and you will see the option to disable it.
Let me know if it helps :)