Well, if running any layout algorithm other than organic layout takes long enough for you to think yEd freezes, chances are your diagram is too large for all the other algorithms.
How many nodes and edges are there in your diagram?
Aside from organic, hierarchic layout is probably the second best option for large graphs. When running hierarchic on large graphs, you should set "Maximum Duration" to "1" on tab "General" and "Routing Style" to "Polyline" on tab "Edges" of the hierarchic layout settings.
Regarding your question to "import with a specific layout somehow", well, it is possible to import coordinates for each node and then use yEd's properties mapper to assign those coordinates to the imported nodes. However, this approach implies that your Excel data does come with coordinates. That is fairly unlikely - especially for large data sets.
Aside from that, it is also possible to import your Excel data without calculating a layout, save the imported graph as GraphML, open the GraphML in another application that is optimized for arranging large data sets, and let said other application arrange your graph. However, all the application that handle large data sets I know of (Cytoscape and Graphviz) use the organic layout paradigm for arranging those data sets.