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Cytoscape.js uses Weaver.js (weaver.js.org) for multitasking. It uses inline-defined workers in browsers.
It's not possible to work around the issue you've mentioned without creating a separate file just for IE10. A major point of using Weaver threads is that you don't have to fiddle with external file references and minfication settings to get webworkers to work.
I don't think it makes sense to add a workaround for a browser that is two major releases out of date, especially since it creates complications for developers using the library.
Your options are:
(1) Fork the CoSE layout with the thread option { disabled: true }. That way, simulated webworkers in the main thread are used. (Make sure to change the name to something like cose-forked so it doesn't conflict.)
(2) Use a layout other than CoSE. There are many supported in the library and many more as extensions.
(3) Tell your IE10 users to upgrade their browser or (better yet) install a decent browser. Chrome can be installed to a user's home directory -- even on Windows.
Looking at the CoSe demo at http://js.cytoscape.org/demos/7b511e1f48ffd044ad66/ , layout fails in IE 10 emulation mode.
Error possible related to http://stackoverflow.com/questions/10343913/how-to-create-a-web-worker-from-a-string
See also parallel-js/parallel.js#12
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