If you install the ES file explorer update directly from their website it will replace the factory one and adds functionality so you can modify system files if you give it root access.
Your phone must be rooted, and you have to enable root access with it in its setup menu.
I would advise NOT deleting these files. If you insist you can simply rename them. Start with telephony.apk. I renamed mine oldtelephony.apk. Then my PE gave me the forced close message. Then I renamed phone.apk to oldphone.apk. Then my PE kept giving me error messages over and over again. I just kept trying and eventually got it to shut down properly (you have about 1 second between error message popups) and once it rebooted no more error messages.
To be honest, I'm not quite convinced it makes that much of a difference. I ran into a problem where I couldn't restore mine but I don't know if it because of me renaming these files or if it was because of an app I installed that it didn't like. I eventually got it working but if you decide to update (or downgrade) the rom I would change those two files back to phone.apk and telephone.apk and then rebooting before doing so just to be safe.
Here is a link to the download page on the manufacturer's website:
http://www.estrongs.com/en/download.html