Um...
Speaking as a player of an artificer as well as an occasional DM, I would actually lay the blame more on the Double Wand Weilder feat rather than the class.
As a point of reference, the Eberron version of the DWW feat is a 3 level prestige class (Cannith Wand Adept) where the ability isn't gained until the 2nd level of the class and burns an additional 1d4 charges from each wand. The class itself requires four feats just to enter.
Also I believe the charge usage is off. While the DWW feat only burns 1 and 2 charges, the Metamagic Spell Trigger ability burns additional charges based on the number of spell levels the modified spell is increased.
The Twin Spell feat increases the spell by 4 levels, so your player should have burned 5 charges from the first wand and 6 charges from the second.
You said 'twinned' in your description so I'm assuming you mean Twin Spell as opposed to Split Ray. Split Ray has a level increase of zero in 3.0. I don't know that it was updated in 3.5 - but since it does what Twin Spell does (better - since you can target multiple people), I don't see why it doesn't have the same increase in cost.
That said, my only other comment is that artificers don't gain gold back for draining magic items - only XP's. She just saves on the XP burn as long as she uses Retain Essence on existing magic items.
I have two question though. Were the two wands crafted as Wands of Empowered Scorching Ray, or just Wands of Scorching Ray? It sounds like she cast Metamagic Item on the two wands to Empower them from your description, but I'm not sure.
My second question is what level were the wands crafted at? A base Wand of Scorching Ray would normally only fire one ray (even if empowered). So using Twin Spell on both wands should have given her a total of 4 rays. The wands certainly could have been built at a higher caster level, but that makes them cost more.
I'm currently playing a halfling artificer whose entire schtick has been that of an enchanted tailor. He makes clothes and only recently has started using/making wands. I'm having fun with him, but he's by far the weakest person in the party and he's currently a full level behind everyone because of previous XP expenditures as well as a death or two.
In your place, as a dm, I'd probably reconsider allowing 3 different sources of feats and classes to work together before I'd ban the class outright.
I admit I'm biased though.
