Pretty much this.
Alternatively, you can press and hold the use key on them to bring up a command interface. Point to a location and tell them to wait there and they will get out of your way.
Companions aren't the issue, as like i said, they are manageable, it's people like guards or non companions that are bothersome. running into them makes no difference, i've tried that. For example i had a quest that i had to go into a small room and the npc followed, like they do when you're in a shop, and i had to wait around 30 seconds before she decided to shift her ass.