Put yourself in her shoes for a minute. She never asked for the Chantry to get blown up and everyone inside it, and now the chantry and Grand Cleric are all gone, by the will of Anders, who is an apostate. Now Meredith has gone completely bananas and wants to execute all circle mages, that includes her, for a crime she and every other circle mage had nothing to with whatsoever. Now imagine your very own brother/sister siding with the woman who's gone bananas rather than taking her side. Remember what Bethany is like, she values her family, Hawke is family, and she's very loyal to her fellow mages, to see her people and family on opposite sides is probably not something she was looking forward to. She is in a bit of a predicament, do I choose my family member and go against my people and feel like I'm betraying my own brethren, or do I choose my people and side against my own family member, possibly resulting in them having to me or me having to kill them. I'll also repeat that she never wanted the Chantry blown up, and she definitely did not ask for psycho woman to open up a can of worms.
Yes, Hawke is in a bit of a predicament as well, just in a different matter, do I serve the better interests of the people or do I serve the better interests of the mages which my sister just so happens to be a part of. You're right in saying that Hawke is in the same situation as her, but Hawke is not choosing between the non-mages of Kirkwall and his/her last surviving family member. You can side with the Templars and let Bethany live, and they let you do that.
My conclusion, same situation, different POV's. That's really all it is.