While watching Doctor Who, I found something that troubled me. The Daleks attempted to blow up the TARDIS; but the last time we saw the TARDIS explode it took the entire universe with it. There was another moment in which the Daleks attempted to destroy the TARDIS at the Crucible. Why did the Daleks attempt to destroy the TARDIS knowing it would blow up the universe and them along with it.
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.
Going way back to the Old Dr Who series the Daleks where always more interested in gaining control of the Tardis in order to use Time Travel to there advantage.
In fact they once built there own Tardis (the Chase).
As discussed Tardis's where destroyed all the time its just the Silence didn't know what they where doing but also created a paradox in which there own actions created the event they where trying to prevent.
If you have an atom bomb, there are several ways to destroy it:
Trigger the nuclear reaction. It'll also take out your city.
Pick an axe and chop it to several pieces. It won't take out your city.
Attach TNT bombs to it and blow it out. Again, it won't destroy your city.
Put it into a gasoline tank and burn it. Again, it won't destroy your city.
You can see here that methods you apply to destroy atom bomb actually decides the fate of your city.
In case of TARDIS also, there are several ways to destroy it. Daleks use methods different from the one used by Kovarian which destroyed the universe.