Not everyone hates the Xenos....For instance, I don't believe that Bretonia Law (police or navy) hate Xenos much if at all.
Here - the list of people you don't DIRECTLY improve by killing Xenos, ripped straight from empathy.ini:
Bretonia Police
Bretonia Armed Forces
Bretonia Mining and Minerals (BMM)
Bundschuh (your rep will actually DROP with these guys for killing Xenos)
Corsairs
Daumann Heavy Construction
Gateway Shipping
Gas Miner's Guild (GMG)
Independant Miner's Guild (IMG)
Kusari State Police
Kruger Minerals
Rheinland Military
Rheinland Federal Police
Liberty Navy
Planetform Inc.
Synth Foods (Your Rep will DROP from killing Xenos)
Zoners (Your rep will DROP from killing Xenos)
Note that this list doesn't tell you the ACTUAL effect of killing Xenos. For instance, the Corsairs
will begin to like you more, even they're listed in empathy as completely uncaring. Why? Two reasons - one, is that the Xenos HATE everyone other than Synth, the Zoners, and the Bundschuh. Since Corsairs are hated BY the Xenos, your rep will go up (they understand the principle of "enemy of my enemy, friend of mine"

. Second, you may be directly raising your rep with factions the Corsairs like (though I don't think this is the case with Corsairs).
However, killing Xenos can hurt your reps. For instance, killing them does nothing directly for Bretonia Police. However, you do raise your rep a bit with a decent amount of factions that hate the xenos which the Police DO hate. For instance, killing Xenos to raise your corsair rep will piss off the Bretonia Police slowly. In reality, this is negated by the fact that you're raising your Bowex rep, but the concept remains true.