The length of the relationships is determined by the results of a physics simulation for the force directed layout. The underlying vis.js library allows for overriding the relationship length determined by the physics simulation: http://visjs.org/docs/network/edges.html , however this is not exposed directly through neovis.js.
I've created an issue for exposing all vis.js configuration options through neovis.js, as this has become a common request. Please track the issue for updates on when this is implemented: https://github.com/neo4j-contrib/neovis.js/issues/36
One option you could try now is the hierarchical layout option, which would replace the force directed layout and may result in a more favorable layout for your dataset: https://github.com/neo4j-contrib/neovis.js#confighierarchical_layout
