EDI and the geth being dead is by all means a very, very real possibility. But a certainty? I don't think so. I think the most likely scenario for the next Mass Effect game is a future set after Destroy. I think it's unlikely the geth will simply be abandoned as a race and will thus reappear. Two and two.
Nothing is ever a certainty, there's no "certainty" that IT isn't real, but that doesn't mean I'll take the possibility seriously. As for the geth, if they appear in MENext, I find it likely they will be rebuilt after Destroy ended them. This would actually be an interesting plotline to explore: provided the details of the Crucible were (now) known, how would synthetics react to a Destroy decision? Would they accept it or reject it? Would they want revenge, something usually associated with emotionality? While I'm not sure I'd be on board with another geth squadmate, I'd certainly be interested in seeing the "next" synthetic generation's reaction to Shepard's choice. After all, my Shepard destroyed synthetics so that synthetics and organics could forge autonomous coexistence going forward. Has he created a future where that is possible, or has his decision precluded the possibility?