For the Greater Good
The first weekend in September 2006, Jack makes the team take a training weekend out of the city, far away from the hub. He knows this weekend is the one: the Doctor, Rose, Mickey and himself are in Cardiff. He knows what happens, that Margaret nearly pulls the world apart. He knows that he and the team can't be there because they'll want to interfere and he can't let that happen. Jack makes sure they're far away, rift sensors left in the hub.
They return on Sunday night, Cardiff is different, there's been an 'earthquake', he sends the team home, makes a copy of the CCTV footage, just needing to see the Doctor and Rose again then wipes the original from the archives and computers. When Tosh complains about it the next day he blames it on the earthquake damaging power lines all over the city centre and his secret is safe.
For the greater good, he protected himself and the team, left Cardiff unprotected because the Doctor was there and he would succeed. He prevented a paradox, kept himself away from the city, away from the TARDIS even when he knew they'd leave it unmanned, away from the Doctor, away from it all.
End