I really have no problems with the Doctor getting 2x stronger without snuffing out the candles. If that was so, everyone would refuse to do that. In exchange of not snuffing them out is taking Lhose's soul for good. I know it was possible to defeat him in his full power, it was difficult not because Adrahmahlikh was twice stronger... but you have limited time and you have to kill him before he takes Lhose. I'd use the Anathema on him the next time I see him in full power.
You can also use skills like clear minded and enrage I think to buy time.
