I'm also still stuck on this problem.
Only way to stop networking that works on 12.04.2 LTS is /etc/init.d/networking.
Restarting networking is also done only by /etc/init.d/networking. 

skomatsu@tokito:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 12.04.2 LTS
Release:        12.04
Codename:       precise

skomatsu@tokito:~$ ifconfig eth0
eth0      Link encap:Ethernet  HWaddr 08:00:27:62:08:36
          inet addr:10.0.2.15  Bcast:10.0.2.255  Mask:255.255.255.0
          inet6 addr: fe80::a00:27ff:fe62:836/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:53193 errors:0 dropped:0 overruns:0 frame:0
          TX packets:30937 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:76448766 (76.4 MB)  TX bytes:2160269 (2.1 MB)

skomatsu@tokito:~$ sudo /etc/init.d/networking restart
 * Running /etc/init.d/networking restart is deprecated because it may not enable again some interfaces
 * Reconfiguring network interfaces...
ssh stop/waiting
ssh start/running, process 16511
   ...done.

skomatsu@tokito:~$ ifconfig eth0
eth0      Link encap:Ethernet  HWaddr 08:00:27:62:08:36
          inet addr:10.0.2.15  Bcast:10.0.2.255  Mask:255.255.255.0
          inet6 addr: fe80::a00:27ff:fe62:836/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:53202 errors:0 dropped:0 overruns:0 frame:0
          TX packets:30952 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:76451045 (76.4 MB)  TX bytes:2162258 (2.1 MB)

skomatsu@tokito:~$ sudo restart networking
restart: Unknown instance:
skomatsu@tokito:~$ ifconfig eth0
eth0      Link encap:Ethernet  HWaddr 08:00:27:62:08:36
          inet addr:10.0.2.15  Bcast:10.0.2.255  Mask:255.255.255.0
          inet6 addr: fe80::a00:27ff:fe62:836/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:53203 errors:0 dropped:0 overruns:0 frame:0
          TX packets:30954 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:76451135 (76.4 MB)  TX bytes:2162418 (2.1 MB)

skomatsu@tokito:~$ sudo stop networking
stop: Unknown instance:
skomatsu@tokito:~$ ifconfig eth0
eth0      Link encap:Ethernet  HWaddr 08:00:27:62:08:36
          inet addr:10.0.2.15  Bcast:10.0.2.255  Mask:255.255.255.0
          inet6 addr: fe80::a00:27ff:fe62:836/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:53203 errors:0 dropped:0 overruns:0 frame:0
          TX packets:30954 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:76451135 (76.4 MB)  TX bytes:2162418 (2.1 MB)

skomatsu@tokito:~$ sudo service networking restart
stop: Unknown instance:
networking stop/waiting

skomatsu@tokito:~$ ifconfig eth0
eth0      Link encap:Ethernet  HWaddr 08:00:27:62:08:36
          inet addr:10.0.2.15  Bcast:10.0.2.255  Mask:255.255.255.0
          inet6 addr: fe80::a00:27ff:fe62:836/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:53203 errors:0 dropped:0 overruns:0 frame:0
          TX packets:30954 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:76451135 (76.4 MB)  TX bytes:2162418 (2.1 MB)

skomatsu@tokito:~$ sudo service networking stop
stop: Unknown instance:

skomatsu@tokito:~$ ifconfig eth0
eth0      Link encap:Ethernet  HWaddr 08:00:27:62:08:36
          inet addr:10.0.2.15  Bcast:10.0.2.255  Mask:255.255.255.0
          inet6 addr: fe80::a00:27ff:fe62:836/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:53203 errors:0 dropped:0 overruns:0 frame:0
          TX packets:30954 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:76451135 (76.4 MB)  TX bytes:2162418 (2.1 MB)

skomatsu@tokito:~$ sudo /etc/init.d/networking stop
 * Deconfiguring network interfaces...
   ...done.

skomatsu@tokito:~$ ifconfig eth0
eth0      Link encap:Ethernet  HWaddr 08:00:27:62:08:36
          BROADCAST MULTICAST  MTU:1500  Metric:1
          RX packets:53203 errors:0 dropped:0 overruns:0 frame:0
          TX packets:30955 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:76451135 (76.4 MB)  TX bytes:2162760 (2.1 MB)

skomatsu@tokito:~$ sudo start networking
networking stop/waiting

skomatsu@tokito:~$ ifconfig eth0
eth0      Link encap:Ethernet  HWaddr 08:00:27:62:08:36
          inet addr:10.0.2.15  Bcast:10.0.2.255  Mask:255.255.255.0
          inet6 addr: fe80::a00:27ff:fe62:836/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:53211 errors:0 dropped:0 overruns:0 frame:0
          TX packets:30967 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:76453324 (76.4 MB)  TX bytes:2164247 (2.1 MB)