Discovery of gravitational waves do not imply the existence of Aether models. Besides, having interferometers in different experiments don't necessarily mean that the same problem is addressed by both.
Aether models were motivated in order to explain the propagation of light in vacuum. People believed that a medium was required for the propagation of electromagnetic waves, and they postulated aether as that medium. However as you mentioned, Michelson-Morley experiment proved that there was no such medium in place, and EM waves travel in vacuum without the need for any model.
Einstein showed that gravity arises due to the geometry of spacetime. The field equations of Einstein admit wave-like solutions, which are referred to as gravitational waves. The recent discovery confirms the predictions.
Why detection of gravitational waves has no relation with the presence of aether
The scope of LIGO and the Michelson-Morley experiment are different. Michelson Morley experiments were designed to detect the change in the speed of light, whereas LIGO was designed to detect the gravitational waves generated by astrophysical events. In simple terms, when a gravitational wave passes through the interferometer, it causes the space to stretch or shrink depending on the arms of the interferometer and this causes a interference pattern to emerge when light passes through the arms.
Now, if the medium would have been aether, the interference pattern would have been produced by different speeds of light in the different arms of the interferometer and would have been detected long ago, not only by Michelson-Morley experiments but also by many other follow-up experiments desined to test the same. All of them reported that the speed of light is constant in vacuum. That settles the case for aether. In LIGO the scope was to detect gravitational waves corresponding to a special astrophysical event by measuring changes in spacetime by passing of the waves through the apparatus. As a result, the finding don't show (or address) that speed of light is not constant in vacuum, as is the case for the validity of aether models (and which has been disproved by many other experiments). Having interferometers in different experiments don't necessarily mean that the same problem is addressed by both.