I just thought of an even better solution - completely ignore the equip command. Instead, you can manually equip the item you want with a memcpy command.
http://www.gscentral.com/codes.pl?dev=par&sys=snes&game=chronotriggerMore memory addresses. Here you'll see that Crono's weapon address is 7E2629xx All the other equip slots, character values, and item values are all on that page.
I assume you want the player to keep their original equipped weapon after the battle is over.
Example:
Before battle:
Assignment, Mem-to-mem, variant 48, one byte wide, to copy from 7E2629 to 7F0240 ;copy Crono's current weapon to temp value
Assignment, Value-to-mem, variant 4A, one byte, Value 01 (Crono's sword) Store to 7E2629 ;equip Crono with Wood Sword
After battle:
Assignment, Mem-to-mem, variant 4D, one byte wide, to copy from 7F0240 to 7E2629 ;equip Crono with his original weapon
That way you avoid all the "bonuses" of the equip command