Midna might have seen it as the only solution.
By shattering the Mirror of Twilight she prevents anything merging from Twilight Realm to Light Realm - and vice versa. People of Light Realm punished Ganondorf and sentenced him to Twilight Realm, causing the events of Twilight Princess. She might have been protecting her own land by destroying the only way between them, because it was Sages' fault that Ganondorf ended up in Twilight Realm. They were afraid to face him - understandable - and their solution to dealing with him was to send him to the other world, where they thought he wouldn't cause problem to Light Realm. Not caring about the people of Twilight Realm in the least.
Maybe Midna just wanted to put a stop to this kind of things ever happening again, did what a proper leader would do - sacrificed something dear to her (I think she saw Link as a comrade more) for the good of her people, who have already suffered.