[UPDATED]I found this http://newvegas.nexusmods.com/downloads/file.php?id=40742 at newvegasnexus that should fix the problem. The author also advice to use the console "SetAlly 1b2a4 118368 1 1 ;Neutral" to return the Van Graffs to neutral instead of installing the mod.
But why aren't there are any in-game warning of the consequence? The Van Graffs have some exclusive energy weapon mods and some unique GRA weapons. They are a essenstial to players who prefer pew-pew over bang-bang. Obsidian should have let the Gun Runner take over their inventories.