It would help us understand better if you gave us the OS version and what tools you have to use for the restore.
In HPUX, restoring from an Ignite tape is very easy.
If using a tar ball, it is equally as easy with a few options that you will need to use.
With dump and restore, it shouldn't be too hard either.
I had the same thing happen about a month ago on a live production box. Someone did "chmod 444 *", very bad!! All of my executables were disabled as well as several daemons like telnet, sendmail, inetd, and others.
I did mine by hand, instead of using a backup. But now that I look back it could have been easier using a backup tape to restore.
It was time consuming, took the better part of a day, but I could not take the box down at the time.
There are several linked executables from /etc to /usr/sbin and then to /bin as well. You will also have to look at subordinate directories as well. There exe parms are probably wrong as well.
As to your question, there should be a parameter of the restore command to keep date and time stamps as well as permissions and ownership.
Now that I think about it, permissions shouldn't change when restoring, but time and date stamps may.
It took me the better part of a day to straighten my 2 systems out, but I did it without using a restore tape. Primarily by comparing the corrupted system to one that was similar and in good order.
After you have restored this box, check it against another box just to be sure.
Also, check to ensure that all of your pertinent daemons are running, namely sendmail, inetd, init, etc...