Found it here: http://forums.ni.com/t5/LabVIEW-for-LEGO-MINDSTORMS-and/spec-file-is-not-read-when-installer-is-run-in-silent-mode-but/m-p/2774740/highlight/true#M2322
Just change your ini file Features section to this:
[Features]
LEGO_EV3_EDU_Feature.EV3.EDU.100=
EV3_EDU_Mode.EV3.EDU.MODE.100=Local
Tested it for my own installations (deploying with SCCM to several teacher machines) and it works.