If a bowler during his runup sees that the batsmen at his end is out of his crease can he run him out before he bowls the ball.
Yes. Law 42.15 in the MCC laws of Cricket say the following:
The bowler is permitted, before entering his delivery stride, to attempt to run out the non-striker. Whether the attempt is successful or not, the ball shall not count as one of the over.
If the bowler fails in an attempt to run out the non-striker, the umpire shall call and signal Dead ball as soon possible.