The NCAA is in a tough spot here.
A proper and thorough investigation of this matter will take years.
So I think the NCAA pretty much had to give the tree a good shake now to see if any irrefutable evidence fell out that they could use, run with, and make stick quickly. That was unlikely to happen.
Short of that, they're pretty much forced to say Newton is eligible now, and if anything turns up down the line, strip him/Auburn of their awards and trophies like Reggie Bush/USC.
Imagine if Newton were to be declared ineligible now, Auburn loses, and then he is eventually exonerated of wrong-doing? "Sorry Auburn" isn't going to cut it if they're robbed of a chance to win a national championship.
It would be better to make a final and accurate determination of the matter now, but with the time frames involved it's just not possible.