It is very counter-intuitive that Anakin should kill or injure Padmé.
The rationale for Anakin joining the dark side was that he could use its power to save Padmé. If that was his objective, why should he hurt her?
Not only is that irrational but it seems here that Anakin is showing human emotions like attachment, anger, frustration and/or indecisiveness. A true Jedi should be in control of his negative feelings.
The novelization is clear that he thought she'd betrayed him:
"Obi-Wan?" She whirled, and he was on the landing ramp, still and sad. "No!"
"You," growled a voice that should have been her love's.
"You brought him here..."
[...]
Anakin's lips peeled off his teeth. "I would thank you for this, if it were a gift of love."
Trembling, shaking her head, she began to back away. "No, Anakin - no . . ."
"Palpatine was right. Sometimes it is the closest who cannot see. I loved you too much, Padmé."
He made a fist, and she couldn't breathe.
"I loved you too much to see you! To see what you are!"
[...]
Obi-Wan knelt beside Padmé's unconscious body, where she lay limp and broken in the smoky dusk. He felt for a pulse. It was thin, and erratic. "Anakin - Anakin, what have you done?"
In the Force, Anakin burned like a fusion torch. "You turned her against me."
Revenge of the Sith Official Novelization Chapter 20
You're absolutely right, though: this is very irrational. In his anger and frustration, Anakin is lashing out, something we've seen him do before, even before he was a fully-anointed Sith Lord. Now that he is one, his lashing-out takes a somewhat more destructive tact.
That being said, by all accounts her death really was accidental; he certainly seems regretful when he learns about it.
