The reason for Marshal Strickland's absence, and for his deputy being the one to arrest Tannen, was due to a deleted scene where Strickland was shot dead by Tannen. However this scene appears only in the novelization, and when Tannen is arrested, it is for the murder of Strickland. The Marshal is said to have been shot and killed by Tannen in Back to the Future: The Game. However, whether or not he was killed, is still under debate since Back to the Future: The Game is not considered as canon.
As the deputy reads the charge "robbing the Pine City Stage", the camera cuts to a shot of Marty McFly and Emmett Brown to cover the fact that this line has been dubbed over the original dialogue, "the murder of Marshal James Strickland".
In the novelization, Marshal Strickland has three deputies (page 178), but in the movie there is only one.