What about the Cytoscape Desktop metaphor do you not like? As one of the original folks on the project I wrote the early API, and we very specifically made it data-agnostic. So unless you don't want to use nodes and edges (in which case yeah... look elsewhere) I think it's pretty adaptable.
When I was doing grad school work while working on Cytoscape the rendering engine part was only for figure generation. Most of the "real" work was using the networks-subnetworks and doing interesting things with the graph model.