If that was all what she did, I'd agree with you, but just this school-year she physically cornered him when he got sick (from being close to her) and pried for her own amusement, and later she called him out for a talk just to roast him over that bullying, doing her "but for me it was Tuesday" impression. While doing that, she also said she'll keep being close to Kusunoki, which, considering what MC knows about snake-girl's character and that Hebikawa already made her bawl her eyes once, can reasonably sound to him as a potential danger to his best friend.
We as a readers privy to their thoughts even know that Hebikawa still wants to make Kusunoki "show her true face", which, considering the last time she tried that, sure sounds like danger to Kusunoki, just like MC suspected. That would make MC reasonable for avoiding helping her unless she's, like, bleeding out or something similar.