I just found out, that you can become the leader, but don't know what it does.

The Khans won't shoot you on sight I guess.

If you have a high reputation with the Khans (I believe you have to be liked), you can be named Papa's heir after you wipe out Camp Forlorn Hope in the quest We Are Legion.

Then, if you sneak-kill Papa Khan (he's pretty much alone only when he's sleeping) you can talk to Regis afterward and he'll confirm you are now indeed the Great Khan chieftain. Regis will ask you what course the Great Khans will take in the battle at Hoover Dam. You can tell him to side with the NCR or with the Legion. You can also give leadership to Regis and tell him to take the Khans and head North, away from the Mojave, during the battle at the Dam. The final option is to tell the Khans to fight for themselves and kill both NCR and Legion, but due to their small numbers this is a suicidal last stand for them. They'll still obey though.

If you choose to not let the Khans side with the Legion, they'll kill Karl on the spot.