No bounty is okay but you have prepared two possible problems in the future. Well, they should not be critical.
1. The boss: Yes, one of the main quests will want you to speak with him. But you can complete the quest by killing him as well. Therefore, killing him now should not prevent you from completing this quest.
Note also that the boss is one of the Hlaalu bosses. If you are a member of Hlaalu then you could have additional problems. I don't know, I haven't played House of Hlaalu.
2. Both the boss and the brothers in the basement: If you are a member of Morag Tong then you will lose reputation. The brothers are the object of a writ and the boss is the object of a grandmaster writ. When it comes to these writs, you will be asked why you have killed them without command and said that Morag Tong isn't a bunch of assassins (well, then what is it
). -10 to your rep with Morag Tong in both cases.
But that's all. You can get your rep back by doing next quests a bribing.
Recommendation: Keep the save before cleansing the manor for safety and continue the game.