She literally states in the film that he has essentially murdered her, she tells the third guy he murdered her. How can you be surprised no one picked up on it. It wasn't subtle, it wasn't left unsaid, it wasn't something hidden away that you had to work out for yourself, it was in your face....
As Tombstone said though, she wasn't murdered, that was her somewhat childish reaction. Her life plans were changed, that happens, you get hit by a car and end up in a wheelchair for 70 years... no one says you've been murdered, even if your life changes completely. She wasn't murdered, just the life she THOUGHT she'd have was 'murdered', but 99% of people don't end up living the life they planned on. Tombstone has a good interpretation, she wasn't actually doing anything with her life, we don't even know she's a good writer. Her dad was a apparently great writer who went out and did everything, she did this trip because she felt she'd done nothing amazing(which loosely implies she hasn't written anything good, if in general the best writers experience a lot before writing anything good) so she gave up her entire life just to write about a colony. Hell, for all she knows the colony would be wiped out after a week, the ship may be unable to get back to earth, earth may have been wiped out by a plague or war before she gets back.
SHe instead found happiness and love, something she seemed to lack. Maybe a good way to put it is, she was searching for something amazing and was unhappy and took the trip just because she thought maybe that would be enough. But trapped on the ship, accepting she can't change it she stops looking for the great story to tell and just starts living her life and being happy Then there is the whole, if he hadn't in fact woken her up, she'd have died anyway. So regardless of him waking her up, she wasn't going to have that life she thought she would.
But ignore all of that, so what, he knew waking her up was horrible, but he suffered from extreme depression and loneliness, he was literally not in his right mind when he chose to do it. He begged himself not to but realised it was wake her up or kill himself. He didn't choose to be woken up himself, he was 'murdered' by the ship, or whoever chose not to make a way for someone to be put back into stasis on the ship in case of emergency.