DalekFlay, mah boi, my main man - I never got the feeling the Geth and EDI were supposed to represent homosexuals. The vampires in True Blood, sure, but the AI's in Mass Effect? The Geth are presented as mindless and faceless killing machines in the first game, while the sequels introduce the idea that the Quarians started the whole war because they were afraid the Geth had become too alive, and the Geth retaliated to survive.
If anything, I'd say the Geth-Quarian conflict is closer to the Israel-Palestine conflict than persecution of homosexuals, as in "Who's right?", "Which side do I support?" and "How do I solve this peacefully?".
And the fear of AI in general is the good old fear of technology (see: Skynet), sometimes well placed as when a rogue Virtual Intelligence took over the Moon in ME1, sometimes not as in the case of EDI who rebelled against her crazy developer the Illusive Man and remained loyal to Shepard, flooding TIM's servers with porn in the progress.