You can make the file named bookmarks a read-only file...
...but if you forget to "unlock it" and you bookmark something, Chrome does not warn you, it just fails to bookmark the site.
Probably a better way would be to put a small batch file in the startup folder for your profile. Have that batch file copy your bookmark file to a place in your documents (or wherever you think would be safe). That way, you would have a backup copy that you could restore.
xcopy "%USERPROFILE%\AppData\Local\Google\Chrome\User Data\Default\Bookmarks" "%USERPROFILE%\Documents\chrome-bookmark-backups\year_%date:~-4,4%_month_%date:~-7,2%_day_%date:~-10,2%_hour_%time:~-11,2%_minute_%time:~-8,2%\" /v
The code above is simplistic and assumes that the date and time is stored mm/dd/yyyy hh:mm