If you are at a point of setting up a CI server then the benefits of bundling built into the Visual Studio seem marginal - I would assume that you are not going to be performing deployments from VS and will be instead deploying through your CI environment.
If that is the case, I would consider turning off bundling in Web Essentials and using a command-line bundling solution such as WebGrease or AjaxMin . I heard that AjaxMin is what is being used by WE and WG anyway.
Another approach could be to leave the WE bundling in place and attempt to use command-line WebGrease to replicate Web Essentials' bundling in your CI step:
wg -b -in:C:\javascript -out:bigjavascriptfile.js