I've recently started my first legion playthrough, all my others ended up indy/House/NCR and I know Caesar has you destroy the BOS but if you have Veronica ditch the BOS will she leave still after you kill them.

You'll be able to keep Veronica Santangelo if you kill all the Brotherhood of Steel members *without* using the self-destruct sequence.

She'll just warn you that this is your last chance- so don't wear NCR faction armour while around her afterwards.

I am surprised she even works with you if you are siding with the Legion but it appears that there is not a condition for that.

Anyway, if you kill the BOS and do not destroy the bunker, then you can keep Veronica as a companion.

Thanks, kind of against RP rules though so I might just use Cass, but I can't bear not having Veronica, my favorite companion in all of fallout.

Cass actually comes across as fairly pro-NCR in her dialogue despite her dislike of its bureaucracy. The only companion that is indifferent or somewhat pro-Legion is Raul. Lily might fit the bill too.