Although it was revealed in a later episode to be a Silence ship as you stated, and almost certainly created for the purpose of their mission to kill or imprison The Doctor, all available information suggests that it was not the intention of the ship's creators or its AI to blow up the universe by luring the Doctor into it.
Remember that the AI told the Doctor:
The ship has crashed. The crew are dead. A pilot is required.
It seems unlikely that the ship would have sacrificed its own crew just to set a trap for him.
Although the AI stated, upon finding the Doctor, that "the correct pilot has been found", this just meant it had found someone it believed to be capable of piloting the ship, not that it had been looking for the Doctor specifically.
Amy asked the Doctor:
Could you fly the ship safely?
To which the Doctor replied:
No, I'm way too much for this ship. My hand touches that panel, the planet doesn't blow up, the whole solar system does.
The humans it had previously lured in were not capable of piloting it as The Doctor also explained. But the fact the Doctor was "too much" for it would suggest that this crude attempt to copy a TARDIS had been piloted by some other alien race, neither human nor Timelord. It had been designed to be piloted, not just as a trap. As the Silence were pursuing the Doctor throughout time and space to kill/entrap him at a fixed point, evidently they were already using time-travel and this was one of those ships. We know that the Silence were on Earth in the 1960s because of the events of The Impossible Astronaut.
It was also explained that the reason the AI never attempted to lure Craig in was that it sensed he did not have a desire to go anywhere because of his secret love for Sophie. Evidently, just as the TARDIS has a symbiosis with its pilot, this replica needed a pilot that consciously wanted to leave. It didn't attempt to pull the Doctor in because of who he was, but rather it sensed the Doctor's wanderlust which is a key theme of the show.
In the end, the ship imploded, not because of the input received from The Doctor, but because of the negative input from Craig who had an overwhelming desire to stay.