bootstrap.CdnFallbackExpression = "$.fn.modal";
Checking for the modal function should work, and seems to be the most common method on the interwebs (e.g. how to fallback twitter-bootstrap cdn to local copy).
That should write out something like:
<script> $.fn.modal || document.write('<script src="Script/bootstrap.min.js"><script>')</script>
If you also wanted something for css, then you could do it manually. This snippet might help: https://github.com/MaxCDN/bootstrap-cdn/issues/110
Or, there's this github project: https://github.com/EmberConsultingGroup/StyleBundleFallback