While it sucks for Tsukina, you can't really fault her mother here. Her teenage daughter drastically changed her normal behavior, started hanging out with an older man, is failing in school, quitting her sports team, etc. What is a mother supposed to think? Especially when Tsukina won't talk about any of it.
Yeah, her miscommunication's pretty bad. I don't remember reading any part where they're bound to keep it secret either. She just has a feeling that she needs to keep it hidden for some odd reason.
I get that coming out as a werewolf isn't exactly gonna guarantee being welcomed by your adoptive parents with open arms (especially in Japanese society with how well-known it dislikes anything that can be "different", seeing as how being born with a different color of hair alone can lead you to be ostracized). But at the same, they're the people that adopted her. They quite literally chose her and they seem to be loving enough to allow her the freedom to rry out new experiences without being overly strict. They would probably ask her to keep it on the down low as well but I don't see them as the type of people to go 180 and hate the MC.
That asids, Tsukina's relationship with Hayate is a bit odd... 3rd year high in Japan is equivalent to our senior year (and they instead have 3 years pf middle school) so MC would probably land around the 16 - 18 range. Meanwhile, Hayate is 20 at minimum, but more likely to be around 23 or so. That's a pretty large age gap.
I get that he's the werewolf mentor. But at the same time, should a mentor really derail someone from attending college when that can literally be the difference between a good and a bad position with how competitive and rough the Japanese economy is?