He wasn't freaking out about people attacking the MC because of his pheromones.
He wasn't comfortable with the idea that alphas and omegas are naturally attracted to each other through pheromones (i.e. fated pairs), which is why he was resistant because he was worried the MC was only attracted to him because of his pheromones.
The MC liked the ML from the start, and this didn't have anything to do with the ML's pheromones (the ML's brother explains all this in chapter 8)
Ahhhhh I guess it was more my misunderstanding from MLs previous reactions when they were in school. Also I didn't really understand what he was talking about because I was focused on that other worker who maybe had a crush on ML? If I'm going based on context clues. I have ADHD and if there's too much dialogue I occasionally miss it and just go based on physical reaction.
If you read the convo at the end of chapter closely, they actually finally did bond as pair. But it wasn't because of pheromones. It was because they both love each other so much. Only after MC was begging to bond with him to be closer to him that he agrees to it. It wasn't shown but it was implied heavily via his brother's perspective. This is important because only ML brother's knows about ML whole outlook on soulmate and bonded pairing.
I think what got me the most was ML not becoming mates with MC even though it would've solved the issue he was freaking out about the whole time lol people attacking the MC because his pheromones but they'd be able to solve that issue by pairing but ML was weirdly resistant to that. Idk unless I understood it wrong it just felt like a stupid choice for them lol