It kind of tricky what you are trying to do... I can think of two ways, although I don't work with Inkscape but Illustrator:
Simple and most obvious, align the circle first and the reposition the line. But I get the feeling this is not something that didn't cross your mind already
Make the member you want to center(your circle) be in the center of the group.
First ungroup your objects and make another group, in this new group add another object...
an invisible line (a object with opacity set to 0) positioned exactly as your original line but in the opposite direction. I have an image to explain this technique :

To position this line exactly as the other line use the Align features such as Horizontal Distribute center and Vertical Distribute center...
Then after you have this new grouped object the center should be again in the center of the circle... hope you understand all this... its kind of ... invented on the spot... but it worked for me.. if you need further explanation just ask! :)
You don't really need to set the opacity of your new line to 0, you can simply delete it after the job is done... I was just thinking maybe you might need it later again so its better to leave it there untill you know you wont need it again, but you set the opacity to 0 so you don't see it...
This is much easyer to do in Flash, where you can move an objects(Symbol in Flash) Registration Point, if that exists in Inkscape... then, just do that...