Once you make Hadin the leader, wait a few days and head back to the hidden vault... a scout should run up to you and say something about changes and blahblahblah, then you talk to the (former) elder and he'll allow you to become a BoS paladin if you do a quest for him. Don't wanna ruin the quest but thats how you ally with the BoS. It doesnt mess with NCR rep or anything either, I'm still good with everyone after allying with BoS.
Um, do you literally mean ally (as in you it is an option on Yes Man), or do you just mean that you are allowed to join the BoS
Because first I put Hadin into power, did the Van Graff quests, joined the BoS and still didn't have the option to have them join me
Then, I reloaded a save and did the long, annoying quest for the Elder and joined the BoS and it STILL did not give me the option to join them
Really frustrating! It feels like as if I missed a big part of the game