I think it depends on your options.
Do you have a boot option for "diagnostics"? If so, I'd boot to that and check the hard drive. There may be other reasons for the repair to take an unreasonably long time but the only one I've seen is a bad or failing drive (or one that the system somehow thinks is bad).
The same holds if you've got a boot disk for your hard drive (Seagate SeaTools or WD's disk). Use that to boot and test your primary drive.
If you're got a recent backup then I'd consider using it (after verifying that the hard drive is OK).
Or, if you don't mind doing a complete re-installation of the OS and programs then you might try that, it will test the drive during the installation process.
Otherwise, if the status bar is still advancing then I'd let it run. That might be the least bad of all the options.