Is there any way to make the nomads neutral in MP?

Yes, and there's a mod out that makes killing Nomads increase your rep with every faction, including the Nomads. It's called Friendly Universe, if memory serves. Have a look at that if you want to learn to mod the Nomads to be friendly.

Mini-Tutorial
how to make the Nomad faction to be a neutral faction with all the others factions

DATA\initialworld.ini
Change, in each group, {rep = *.**, fc_n_grp} to {rep = 0, fc_n_grp}
Change, in the group fc_n_grp only, all the {rep = *.**, ****} to {rep = 0, ****}

EXE\newplayer.fl
Change the line {house = -0.65, fc_n_grp} to {house = 0, fc_n_grp}

EXE\mpnewcharacter.fl
Change the line {house = -0.65, fc_n_grp} to {house = 0, fc_n_grp}

data\missions\empathy.ini
Change, in each group, {empathy_rate = fc_n_grp, 0}
Change, in the group fc_n_grp only, all the {empathy_rate = ****, 0}

Fully neutral nomad with all the factions

ps: the friendly universe will do: if you kill 20 nomads every faction, including nomad, will be fully friendly.

It would seem, if you kill over 180 to 200 Liberty navy fighters, you become white to the ones in Unknown via Gamma....worked for me.