I naturally carb my kegs when the pipeline's full enough. My procedure looks like this:
Add sugar to sanitized keg, rack beer onto sugar. Close keg, purge headspace 3-5 times with CO2, ignore the keg for a few weeks.
You don't need to leave air in the headspace to get the yeast to consume the priming sugar. Also, I've primed several kegs where I forgot to purge the headspace, without ill effects.