Well, it is possible to force the hierarchical layout algorithm to keep the order of connectors as is. (See "Tools" -> "Constraints" -> "Port Constraints" with "Configuration Method" set to "From Sketch".) Of course, this requires the connectors to be already at the desired geometrical position (relative to the corresponding node). This means you will have to generate appropriate port locations for the edges in your GraphML. E.g. in
<graphml ...>
...
<graph>
...
<edge ...>
...
<data ...>
<y:PolyLineEdge>
<y:Path sx="15.0" sy="15.0" tx="-15.0" ty="-15.0">
...
</y:Path>
...
</y:PolyLineEdge>
</data>
</edge>
</graph>
...
</graphml>
the sx, sy, tx, and ty attributes specify the edge's source and target port locations (relative to the center of the corresponding source and target node).