The Federation and Cardassia were allies. There was no reason for Seska to have acted like she did. Legally Janeway had to welcome Seska with open arms, and protect her from any of the Maquis who might have felt betrayed. Her Cardassian rank, if it was high, might have forced out lieutenant junior grade B'ELanna Torres from her position of Chief Engineer, or for Tuvok to give up one of his jobs. Tactical and security are two jobs.