We only know of one instance where the destruction of a Tardis destroyed the universe, specifically in The Pandorica Opens and The Big Bang. We know of other instances where Tardises have been destroyed, as House is littered with broken Tardises in The Doctor's Wife. From that alone, we can conclude that it is possible to destroy a Tardis without taking the universe with it.
Further, there is this dialog from The Journey's End:
DOCTOR: We'll have to go out. Because if we don't, they'll get in.
ROSE: You told me nothing could get through those doors.
JACK: You've got extrapolator shielding.
DOCTOR: Last time we fought the Daleks, they were scavengers and hybrids, and mad. But this is a fully-fledged Dalek Empire, at the height of its power. Experts at fighting Tardises, they can do anything. Right now, that wooden door is just wood.
This pretty clearly demonstrates that where destroying Tardises is concerned, the Daleks know what they're doing.