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.