H, there,

according to the strategy guide your identity is also influenced, whether you kill "the alien" or not.

But what Alien are they talking about?

The Drogg can`t be it. I has to be killed to get the suit-cube. The learner can`t be it either.

Is meant bei "the alien" this flying thing in the room with Dr. Esher?

It's the learner. You CAN kill him if you attack him right away, before he lays hands on you. He doesn't even fight back, just dies from first hit afair. Not much point of doing it unless you want to change your identity to a killer : )

The alien hoverbot flying around dr Esher doesn't count. You can spawn as many of them as you wish in the tube central room.