because she has been traveling in the tardis(or something like that) then why couldn't she remember Rory? dont tell me is because he was is traveling also. either way the doctor left that detail out. someone care to explain?

The Doctor said that she rembered the clerics because they werent from her time, and that her history was being changed due to Rory being erased.

It was because the clerics weren't from her timeline but Rory was

Why could River remember then?

For the same reasons - she had clearly at some point travelled in time (implied, but not yet verified - possibly with another Doctor before she was imprisoned) so she sees the universe differently. As she was only with the soldiers for the same length of time that we were, they had no direct influence on her specific timeline. Indirect, yes, but not direct.

The plothole is Father Octavian in that instance, as it's to him that she is released...

But River Song would remember Father Octavian as he wasn't taken by the Crack, he was killed by the Weeping Angels.

The problem is that either Octavian's body would have fallen into the crack with the Angels, or the circumstances of his death would have had to change, as the Angels wouldn't have killed him.

Just to expand on this, Amy actually asks the Doctor the exact same question as the OP. To which the Doctor replies that Rory was part of her personal history, the soldiers were not.