I can't imagine having thrown Ebon Geists at my party while they were Rank 1, certainly not aboard their ship, though such a thing is surely possible when using Navis Primer.
If I remember correctly, one specially lucky Ebon Geist managed to kill/incapacitate 12 guardsmen, knocked down the AM (who failed miserably on the fear test) and ripped off the RT's right arm (who had to burn a Fate point to stay alive) before reinforcement arrived (the geist wasn't killed, just ran away).
Eh, that's just bad luck, happens. Something the players will have to get used to by either accepting it or planning well enough so luck doesn't play a roll (pun intended) anymore. Although if the players are not liking it, you might still want to think about toning it down at least a little bit (GMs can fudge numbers after all... I do it all the time on this side of the GM-Screen )
I just threw 4 ebon geists against my group of 5 players (the 6th, the RT was absent) and they came off just about okay... taught a lesson about power armour not being the best starting acquisition
About that, I want to know more... did they use some tricks to try to tip the Chances in their favor? Was it a square fight 5 vs. 4 at the same time? How many Inferno Pistols did your players have?
Oh, and yeah, Power Armor is pretty useless in most situations.