The component weapon and the target weapon must be different weapons
I don't think that the emblem of greed spell's "description confirms the target is the material component." The spell's description, in part, says
You transform one melee weapon into a burning glaive. The target of your spell must be a masterwork or magical melee weapon appropriate to your size.… If this spell is cast on a magic weapon, the powers of the spell supersede any that the weapon normally has, rendering the normal enhancement bonus and powers of the weapon inoperative for the duration of the spell. This spell is not cumulative with greater magic weapon or any other spell that might modify the weapon in any way. This spell does not work on artifacts. A masterwork weapon’s bonus on attack rolls does not stack with an enhancement bonus to attack. (Emphasis added and irrelevant information about scaling deleted by the answer's author.)
I don't see anywhere in that description that creates an exception to the normal rules for Magic (q.v. Components). While the spell's header material does have the entry "Components V, S, M (a masterwork or magical melee weapon)," that doesn't need to be a reference to or even interact with the entry "Target 1 masterwork melee weapon touched" or with the spell's description of the spell's target. Using the same language doesn't necessarily mean using the same weapon, and I'd argue such is the case here. Read this way, the spell's playable (albeit still problematic—see below) and doesn't break any rules.
Step by step, then, when the caster casts the spell, a magical or masterwork melee weapon that the caster designates that's already in the caster's hand is annihilated as the spell's material component. Then the caster touches a different magical or masterwork melee weapon (because the first one's annihilated), and that target magical or masterwork gains the effect of the emblem of greed spell.
To be clear, "a masterwork or magical melee weapon" remains a problematic material component but not due to its cost. Many spells have expensive material components, although many of those spells seem more generally impactful than this particular spell. (The forcecage spell's 500 gp component sprang to my mind, for example.) On the other hand, being able to annihilate any masterwork or magical melee weapon you're holding is kind of a big deal. You may already realize that your example is both better and worse: Using this reading, if the disarmed warrior's intelligent +5 vorpal longsword or whatever magical melee weapon can be passed to the wizard, the wizard can cast emblem of greed to vaporize that melee weapon as a standard action. (And, by a technical reading, that aspect of the spell works even on Excalibur or Stormbringer!)
I'd argue that few wizards would be willing to spend 300+ gp to cast this spell for its conventional combat reasons, but some wizards are weird. (And maybe they follow up with a transformation spell, I guess?) However, tell a wizard there's a spell that can destroy any melee weapon, and, depending on the campaign, that may be a first-pick spell.