Objectively? No, there isn't a penalty for grinding. However, recruiting/fusing new demons and changing your magatama around is much more efficient than grinding levels/exp when it comes to beating bosses.
Yeah, don't worry about messing up builds, either for yourself or especially for your demons. Inefficient builds may make the game more challenging, but it'll never make the game unbeatable.
I can only think of one situation that might make the game unwinnable, and it has nothing to do with messed up builds.
So, how buffs/debuffs work in Nocturne is that each buff/debuff can be stacked 4 times, and buffs/debuffs last the whole battle unless you negate them. You can makakaja 4 times, you can tarunda 4 times, etc. So, normally it takes 4 casts of each skill to fully max out your buffs/debuffs. War Cry and Fog Breath are a bit more powerful in that they're the equivalent of 2 debuffs (one war cry is 2 tarundas, and one fog breath is two sukundas). So you only have to cast them twice to fully debuff an enemy.
Because of this, while there are some situations where I would take makakaja, most of the time keeping War Cry is the correct choice.
Glad you're enjoying Nocturne btw. As you can probably tell, I fucking adore this game.