There are also other artificers
Don't forget that there are also other artificers. They have access to some infusions that can do bad things to constructs, including warforged and their minions. Get a list of the 3.5 ed infusions for artificers. I would also think that an artificer can create objects which do nasty things to constructs (hold, damage, render inert, etc.).
In order to create objects, the creator has to have some alibi as to how they understand the properties they intend to imbue in their objects. You can't put a "bane" on a weapon against some type of monster unless you really understand their nature. Just passing a knowledge check doesn't cut it with me, you have to convince me you have the experience in your history to justify the possession of that knowledge. To put a bane vs. demons on something, you probably have to have been poking at a captured demon for awhile or access to some really enlightening tome or prior research of others. Same goes for other types (undead, outsiders, etc.)
To imitate spell effects, you have to have access and time to study said spell, whether it be through some mage/cleric or a recovered spell book, etc.
To make stuff you also have to have the appropriate tools. Unless you put a lab in a portable hole that you carry with you, I think alot of advanced crafting isn't going to be possible during an adventure.
By the way, other artificers can create weapons which are a bane to constructs.
For an artificer, you really have to insist they justify having the knowledge, time, and gp to create stuff.
And anyone who has all that nice stuff is going to become known far and wide, and become a target for others who want that stuff.
Also, think about what would happen if this scenario was real. The other players, angry with or frightened of this player, would abandon it if they were intimidated. That's one threat...the players take some opportunity to ditch it, effectively putting him outside the campaign unless it can track them down *grin*. You can tell him you don't have to time to run two parties, them, and a lone warforged.
How about a construct or artificer specific curse?
An area of effect dispel magic could do interesting things to all those enchantments for a little while, also.