Even if they are on top of each other, if u zoom in, you can kill only the enemy radar and not your own.

Use the target circle, right click with bombers so you can make adjustments without actually sending the nuke off, then you can just set the nuke target (left click) when you have got it right:

the nuke radius has to cover the center of the enemy radar but not the center of your own. the black dots in the pic are the centers.
And here it is:

Uploaded with ImageShack.us