If its kihon kote practice you should be going straight through and motodachi should be moving to one side or the other, it is bad habit to 'go around' the person, though in jigeiko or shiai you often have to find a way to get through and the best way to go will depend entirely on what your aite (opponent) is doing.
Kendo-Guide.Com: Thanks for the good comment. Matt is exactly right. Kakarite (striker) should not go around his/her motodachi but motodachi should give kakarite way.
Basically, you should turn without showing your back to your opponent. So if you pass through your opponent?s left (your right), you should turn where your opponent is, which is on your left. So you turn around to the left.
If you pass through your opponent?s right (your left), you should turn around to the right.