While it is true you'll "waste" more Co2 in the headspace with only 2 gallons in the keg, it's a non-issue.
It will likely carb faster, and you will have to purge more to get the o2 out. However, the "Wasted" gas in the headspace is no different than a full keg.
When a full keg kicks, you have still "Wasted" the Co2 in the now empty headspace.
You're good. There's really nothing to worry about.
It could be argued that you'd be better off with 3 gallon kegs for short batches. But, you can buy a LOT of Co2 for the $75 price difference in kegs.