No, she's thouroughly convinced it was Sovieshu's prior to having a paternity test, and even then she dismisses the results (though its difficult to tell if she's in genuine denial or just knows that the baby not being Sovieshu's strips her of her postition and power).
But SPOILERS FOR THE END OF THE NOVEL
Spoiler!
Sovieshu does end up using the fact that the baby isn't his to both depose her as empress and charge her and the Rimwells (minus Lebetti and baby Ian) with treason. The Rimwells are executed by Sovieshu and Rashta recives lifetime imprisonment in a small tower and commits suicide soon after.
