Hell if I know. I only take her at her word. "I may not like it...but now is not the time for ideals."
That, and knowing her from my own DAO playthrough. Which will vary between all of us.
I think...
what cassandra want (and I got that after doing the seeker quest)..is that , she want to find the true meaning of faith . the true mission that the maker bestowed upon the chantry , not just build cathedral.....bow to divine and cleric..and have seeker bodyguard . She say something like that....
That they should seek the true purpose....look more...maybe go farther in the world.....learn from others to find who they are..test your faith..and so on....
edit: she also say..she want the chantry purpose to be involved with the poor..to be a healing and a conforting house..not rich and filled with politic and scorn. And I agree with her..even if..I dont like the chantry as such . I think..thats what religion in general should be..if it must exist .