If you had static sites, it might make sense to check the files on the frontend, but if you have a dynamic site like a CMS, it will be very hard to detect changes via crawling, because by definition the pages should be changing their content frequently.
On the backend, you can check that your code has not been hacked or modified by using file integrity monitoring software, like tripwire. This would let you know if someone changed the source files, added new files, etc. However, this will not help you detect reflected XSS that is in the database, etc. You could write some scripts to check database integrity.
However, if you have vulnerabilities that allow getting root privileges they may be able to then turn off the file integrity monitoring. If you run your webserver in a chroot/jail, this could reduce that likelihood.
Where possible, you might also want to look into migrating your information-only content to a static site generator like jekyll or pelican. This would help you reduce your footprint.