People joking about Naoto having a crush on Kenji, but I feel a need to remind people as to why he more or less NTR'ed Kenji in the first place.
He was looking to protect Kenji from manipulative women, but engaging in threats or violence would not only be ineffective, it also wouldn't fly with Kenji. So he'd dominate them via sex, bring them to heel, and nonlethally remove the threat with Kenji none the wiser.
With Aria and Yuno, he knows from firsthand prior experience that both girls are 100% genuine in their feelings towards Kenji. Neither wants to use, manipulate, or hurt him. So as far as Naoto's concerned, they're both good options for Kenji to shack up with and he's genuinely happy for them under that assumption.
This new girl however, whom he doesn't know, is a complete unknown who's already throwing herself all over Kenji. So for a cynic like Naoto, that's immediately setting off red flags that she's another manipulator pointing Kenji at her enemies like a weapon. Or more accurately, a dog on a leash.