If you go to Setting\Apps\Chrome and scroll down to "Launch by default" and hit "Clear defaults" it will stop automatically opening in Chrome and will ask you which app to open it with when you hit "Yes/Maybe/No". However, if you try to open with Calendar it still goes to the browser with the same issue.
One workaround I have found a work around - there is an app called Invitation Plugin. It allows you to open the invite.ics from gmailGmail and view the event directly in Calendar.
It's a work around for a problem that didn't exist in Ice Cream Sandwich but now does exist in Jelly Bean and really shouldn't exist at all but at least it's a simple and effective work around.