Without destroying BoS?

I REALLY don't want to do it. Through both games I definitely feel my character has an affinity with them and as much as I want to fully complete this part of the main quest, I'm not destroying the Brotherhood.

Sadly no. If you want to get all the goodies the BoS has to offer, it's best you do it beforhand.

The only ways to avoid destroying them are to side with the NCR while keeping the original Elder (and doing all his quests) or side with Yes Man. They are a threat to everyone else.