I agree that you should choose the smaller bike. Most bikes in the country are typically 125cc. A 250 will be huge in comparison!! I rode all over Cambodia on a Honda Bonus 125. Wish I had a 250 as that 125 isn't very off road capable (but it did great on road even 2-up).
On another note, and this may depend on your rental agency, but I hear it's pretty difficult to take a Cambodian bike across the border. You can take a Vietnamese bike anywhere, but Laotian or Cambodian, that may be a different story.