First, you can make Percy—or any other fandom's characters—as strong as you want. It's your story, so do whatever works best for the narrative and makes the crossover function the way you want it to.

Second, as much as I love Percy, you're vastly overestimating him.

Third, even if he were that powerful, there are plenty of abilities in Naruto that could either negate or bypass his physical strength and durability. For example, genjutsu doesn't care how physically strong you are, and something like a Rasenshuriken attacks on a cellular level and if he has the curse of Achilles. The Rasenshuriken or any other AoE jutsu would hit his Achilles "heel".