Overall, I think the 2.3 Ecoboost will be gone from the Mustang line in a few years.
It's not the Turbo 4 that will be gone in a few years, but the V6. I do agree though that the 3.5L EB V6, or even the new 2.7L EB V6, would be a cool option in the Mustang.
The EcoBoost in the Mustang is a ploy to boost Ford's CAFE. The fuel used during Idle and low-speed Traffic is greatly lower from a 2.3L Turbo than the 3.7L V6 and 5.0L V8.
Ford knows that a 4cyl Mustang won't sell, not enough torque from small displacement, therefore it makes perfect sense to offer the Turbo 4 with as much power as the V6. Performance is the same or better than the V6, and even better than the V8 at low rpm's, while achieving better fuel economy than the V6.
The V6 is likely only still being offered while buyers and reviewers figure out that they aren't losing anything when choosing the Turbo 4, and to encourage buyers to choose the Turbo 4, they removed almost all the packages/options from the V6 model.