Is Ecco a morally grey antihero? No he doesn’t. He stops an alien life form from continuing to use the oceans as a buffet. He saved life on earth, not just other dolphins. In 2 Trellia pulls ecco out of his timeline, basically tells him that since he made the aliens aware of the planet by killing one sentient life never evolved and the sea never came to life. In Trellia’s timeline Ecco’s pod all died, the aliens just fucked off, and everything went great. First off Ecco’s pod didn’t die, he lived with them for a time in between games and had children. That’s how Trellia exists because she’s his descendant, so even though he doesn’t return to them after ToT we know at least a good portion of them survive.
Second, Ecco’s time traveling is a closed loop where Trellia’s future is the real one and the Vortex future is a splinter. We know that in Ecco 1 the events of 2 have/will take place again as they always have. Because at the end of Tides of Time Ecco chases the Vortex queen into the distant past where although he isn’t able to kill her completely, he’s able to reduce her to such a weakened state that her and her offspring are forced to adapt and live alongside earth’s other species and eventually evolve into arthropods.
So, since in Ecco 1 there are already members of that order such as trilobites and crabs around we know that the Vortex were/will be defeated in the distant past. They will always show up to take his pod, but Ecco will always defeat them. He’s not morally grey at all, he saves the planet from being regularly fed upon and we on land have Ecco to thank for bees, butterflies and other pollinators that make life as we know it possible. Ecco 1 is pre any time travel, we aren’t playing a post-loop 1 just because we’ve played 2.
Ecco 2 literally shows you that humans never evolved in Trellia’s timeline, and the sea is literally sentient and wills itself into magic sky tubes for fish to swim around in. Ecco 1 pre-disruption was our timeline(there’s even evidence of human life). He destroyed it/us in both the bad timeline(a splinter as you call it) and the timeline Trellia pulled him to/from.