As others have noted, it really seems odd to use equivalent exchange to swap Intuition with Clean. For combat, Intuition is clearly more useful.
That said, since it's an equivalent exchange, can't he just swap it back once he's done cleaning? Also, clean is not a skill he can obtain from eating monster meat he's cooked, whereas I would expect him to be able to easily regain the skill intuition by fighting monsters. In fact, he could really abuse this: kill a monster, dismantle it and cook it, start eating, gain the skill, use equivalent exchange on the gained skill, continue eating, gain the skill again, use equivalent exchange again, take another bite, etc. That said, we don't know how equivalent exchange works; could he choose any skill? How did he get to be able to replace intuition with clean?