I think I am not able resolve your issue. I found something weird on your system.
1. Remove httpd and install again will appear:
Running Transaction
Installing : httpd-tools 1/2
error: failed to stat (deleted) /var/named/chroot/etc/named.rfc1912.zones: No such file or directory
Installing : httpd 2/2
Error unpacking rpm package httpd-2.2.25-1.el5.i386
warning: /etc/httpd/conf/httpd.conf created as /etc/httpd/conf/httpd.conf.rpmnew
error: unpacking of archive failed on file /usr/sbin/httpd: cpio: rename
Installed:
httpd-tools.i386 0:2.2.25-1.el5
Failed:
httpd.i386 0:2.2.25-1.el5
Complete!
where have 2 error:
a. error 'failed to stat (deleted) /var/named/chroot/etc/named.rfc1912.zones: No such file or directory' -> I don't know why
b. error 'unpacking of archive failed on file /usr/sbin/httpd: cpio: rename' -> install/reinstall httpd will be create /usr/sbin/httpd, httpd.worker, httpd.itk and httpd.event and your case 'old' httpd file not able to rename. Why?. It's because permissions of this file 000. If I try to change to 755 and then found 'permissions denied'.
c. In your server, only have 'httpd' file and possible other file like 'httpd;520e560c'. No exists files like httpd.worker, httpd.itk and httpd.event.
I am worry it's related to hacking but I am not sure.
2. At this condition, your vps only use nginx or lighttpd where apache will be not work.
3. Better backup your data and then reinstall OS and Kloxo-MR, except you found someone to fix your issue.