Here's the thing about an Ocean Palace ending:
Because of Chrono Trigger's unique ability to bend continuity by defying the fourth dimension, such an ending would most definetely work. The only issue is that, well, there's still more game if you wanna lose and go see it. But that's about it.
You see, beating the game there would cause time up to that point to break off from the expected path and skew into another tangent...
...most likely? You wake up somewhere in Zeal, with Schala looking after you. Up until now, she's been pretty gentle yet scared, so when this most unexpected slaughter occurs, she is simultaneously amazed and grateful: You've just saved Zeal where she could not. You've done the impossible, and Zeal will continue to soar because of it. As for the Queen? Some say she used to be okay, so with time she might actually turn back to normal.
...Janus however is an interesting case. One of two things can happen at this point.
1: Janus was still cast into the middle ages during the battle, the Prophet opens up to his family.
2: The Prophet/Magus vanishes into the future of Zeal, and nobody remembers him. Janus is unaware.
This is highly debatable of course, but changing history is changing history. In any case, stopping Lavos here and now is probably highly favorable for the Fiendlord. Almost like waking up from a long dream.