There are attributes that you can set in your d3.layout.declaration() that will allow you to deal with the overlap, such as:
var force = d3.layout.force()
.nodes(nodes)
.links([])
.gravity(0.05)
.charge(-1500)
.linkDistance(100)
.friction(0.5)
.size([w, h]);
Important note: I borrowed data from somewhere else and ran the code. So, the values above will need to be tweaked by you. Hope this helps.