The AAT is a subdivision of the Adeptus Terra, and as such always "slaved" to a higher authority with no chance to "infiltrate" it with its own members. Granted, Vandire was from the Administratum, and we know what he was able to achieve - yet this was done by the aforementioned infiltration and clever use of the Administratum's own control of the Imperium's bureaucracy to curry favours or sabotage opponents. It is much easier to hide political scheming behind red tape and possible mistakes than astropathic communications being altered or simply not passed on at all, for the latter is only possible by direct intent and has way less people (and thus possible scapegoats) involved. Not to mention the stigma automatically being a cause for suspicion if anything goes wrong, whether the psyker actually had anything to do with it or not.
Furthermore, Navigators can only be born from intermarriage, making the Navigator Houses incredibly important as a "breeding pool", whereas new Astropaths can be picked up on almost every single world in the Imperium, the only problem being their training - though this potential issue could easily be circumvented by forcing captive survivors of a purge to train the next generation. If Navigators were as numerous and easy to "produce" as Astropaths, I'm sure they would have a harder life and considerably less influence, just because they become replaceable. The smaller Navigator Houses are likely at the mercy of various Imperial Adepta as well, for anything affecting them affects a much smaller portion of Imperial ships, compared to the major Houses that service many more "clients".
Similarly, an Astropath posted to some random backwater world has no connection to his or her organisations' leaders on Terra, so why should they care if the Imperium removes the latter as potential threats to another organisation's superiority? They are essentially living in a gilded cage, more tool than human, which surely affects their "sense of belonging" as well. And without your organisation presenting a unified front against its rivals, you can forget about political power. Most psykers probably do their best to retain as low a profile as possible.
At least, that's how I would interpret it.
Edited by Lynata, 17 January 2014 - 12:59 PM.