I think there are several reasons why she doesn't want them around. She/The Inquisitor can't control them. Unlike the Templars, at this point in the story, The Wardens answer to hierarchy of superiors. Also, they have their own callings (pun intended) and motivations regardless of what Vivienne or the Inquisition would plan for them. They are temporary allies and will not always serve the Inquisition.
Another reason is their Blood Magic. The Warden Mages do not answer to the Chantry and are unrestricted in their use of Magic against Darkspawn as we have seen various examples of throughout the series. The Joining itself is a Blood Magic Ritual. While it could be argued that their actions at Adamant were unethical, it was nothing new to the Wardens.
Perhaps the greatest reason Vivienne dislikes the Wardens is the freedom their Mages enjoy. The Wardens are most diverse organization known in Thedas and not only have Elves, Dwarves and Humans working, cooperating and living together but Mages as well.
Vivienne's pro-Templar point of view reveals it's true nature over time: She doesn't really believe in the Chantry's doctrines on the subjugation of Mages but only her personal power and her place in the hierarchy that those doctrines have created. The Wardens, a powerful example of Mages and mundanes living together without restrictions, something that the Chantry would say is too dangerous, is a threat to those doctrines and thus Vivienne's power.