The best thing to do is let the process run it’s course, as it may take a while and you don’t want to interrupt either the initial scanning for drive problems, or the repair attempts assuming any issues have been discovered on the drive. The repair process can take a while if there are a lot of errors on the drive, but oftentimes there are no problems found and so there will be nothing performed.
Once booted into Recovery mode you’ll find the limitations on Disk Utility’s repair function has been removed, and you can go about repairing the boot disk as intended. The trick is to boot the Mac into Recovery Mode first, and run the Repair function from there.
While this is still the case while booted in most versions of Mac OS X, you can repair the Mac OS X boot disk thanks to Mac OS Recovery Partition, preventing the need from using an external boot drive to repair the disk.