Was that plot element introduced in the sequel (Quake IV) or were they supposed to have been doing this already in Quake II? If this was new behaviour, how was it motivated?
There is a level in Quake 2 called "Detention Center" where you can see a lot of soldiers being processed / killed / assimilated into strogg soldiers as I remember. There is no information about when it started however. Even the Quake wikia page does not have information about this I think that this will remain a secret.