The question - on Lisa or on Maya, does not make the big difference in this case - is whether you really have to use pppoeconf instead of Network Manager or instead of wcid?
One particular setup where I had to use pppoeconf
In the good old days when I did not have a Fritz! Box which acts as router, dhcp server, firewall, dsl modem etc pp, but only a dumb DSL modem, in those not so comfortable old days, it was the Linux system which had to authenticate with the DSL provider directly, because the dumb DSL modem could not do so.
This was the only situation in which I had to use pppoeconf in order to setup the required configuration on my local Linux machine.
Once I had done so, Network Manager would recognize my wired interface had been configured by some other software and refuse to touch it. So I never had to kill Network Manager.
All other usage scenarios covered by Network Manager
Ever since the DSL modem has been replaced by a Fritz! Box (router, dsl modem and more) it is the Fritz! Box which establishes the connection to my DSL provider and which performs the authentication.
Ever since this time, pppoeconf has been sent to retirement on all local Linux machines. It is no longer needed.
With respect to wired connections, simply plugging in the cable and waiting for Network Manager to do its job is sufficient.
With respect to wireless connections, there is a one time setup (select the desired WLAN network, enter logon credentials, tick the option to auto-connect). Ever after there is no need to tinker with anything.
So the crucial question is: What is your network setup? Why do you have to use pppoeconf at all?
Provided you really have to use pppoeconf, in this case Network Manager should not touch the corresponding network interface at all.
If two programmes, pppoeconf and Network Manager, try to configure the same network interface this will inevitably cause trouble.
At the time being network configuration is performed with the help of Network Manager on my machines that run
+ Ubuntu 10.04 Lucid Lynx
+ Linux Mint 12 Lisa
+ Linux Mint 13 Maya
Enlightened by Lucid Lynx, enchanted by Maya Mint, productive on Precise Pangolin's Minty sister