Afraid so. The real sad thing is that his story continues in Radical Dreamers but the creator had that game made non-canon due to Chrono Cross. Magus was originally suppose to be in CC but was removed mid-production in fear the player would exclude using the rest of the characters for him instead. (they would be right )

That line bugged people for years. Many thought it concerned Lucca's mom but even doing that quest doesn't change the dialogue. Only after finishing the Black Omen does the dialogue change.

For a real amusing ending though... in New Game+ After the incedent at the Ocean Palace. Choose to have Frog kill Magus and then defeat Lavos before getting Crono back... Its pure comic gold...