Do NOT climb to the top of the pagoda if you want to complete all four Enemy Skill materias. Only Materia Keeper (whom you've already killed), Godo (whom resides at the top of the Pagoda), and a Stilva (at Gaia mountain that you can only climb once) use the Trine ability. If you want all four E. Skill materias full, then wait until you've gotten all four materias and equip whatever one DOESN'T already have Trine for Yuffie's battle against Godo. You'll also have to be very careful not to kill him too fast at that point, because he may not get the chance to use Trine on you.

Of course, if you don't care, then you're like any other FF player. Go ahead and fight Godo and receive the Leviathan materia.