I'm making an assumption that at some point Thomas will not only leave Demonreach prison, he will somehow manage to balance the scales with the Swartalves, so they're no longer invested in killing him. Then again, for all we know the Swartalves could get wiped out. No one is safe, and it happened to the Red Court so there's no reason it couldn't happen to them. That would solve Thomas' problem too, though not in a very satisfying manner.
Once that issue is dealt with, how long must Harry keep it secret that Thomas is his half-brother? Harry isn't a member of the White Council any more. Other than not overtly breaking the Laws of Magic, Harry doesn't have to play by their cultural rules or worry about their politics. Unless they decide to kill him, of course. However, the one person it could hurt is Ebenezer; so, maybe I'm wrong about Harry not having to worry about White Council politics. However, I'm not expecting Ebenezer to be around much longer, and once he's gone that issue disappears.
Rather than undermining Harry I think the White Council may have actually empowered him by cutting him loose. Any one else agree with me and can you think of another way no longer being a member of the Council may benefit Harry.
Oh yea, if Harry allows his family relationship with Thomas to become public, it takes away the leverage Lara has of knowing the secret.