I think it's more difficult to complete the mission without taking down, tranquilizing nor killing people. Does it gives more points?
Taking down enemies in DEHR can yield up to 50 experience from a single enemy. Considering the ghost experience bonus is only 500 and the smooth operator bonus is only 250, that means if you take down more than 15 enemies per mission using the optimal method, you will always come out ahead experience wise (not to mention that you can still earn Ghost while taking down every enemy in your path).
For more information, this answer has all the experience boosts you can gain when taking out an enemy.
Finally, there are no experience bonus for completing a mission without killing any enemies (though there is an achievement for doing this through the entire game). Like I said above, are bonuses for ghost and smooth operator but those are not mutually exclusive to takedowns.