Is there any benefit to sparing feral ghouls during Come Fly With Me?
It looks like there is no direct benefit to sparing the ghouls in this quest. After replaying the quest using stealth and a pacifist approach there was no comment on or reward for the preservation of the feral ghouls.
As remarked in the comments it is possible to earn an extra 200XP for saving Harland and nonviolently removing the nightkin from the basement. Such a bonus does not seem to exist for ignoring the feral ghouls.
Notably, after completing the rocket launch the feral ghouls that are inside the Repconn Test Site are gone, taken on the Bright's Great Journey. This is also recorded in Come Fly With Me's wikia page:
Any feral ghouls that you didn't kill inside REPCONN will join the "Great Journey." Feral ghouls that you didn't kill outside REPCONN will still be there and be hostile.
The only benefit to be gained from sparing the feral ghouls is the conservation of ammunition and medical supplies that would normally be consumed while fighting them.