I was just thinking that earlier today! 100% support this idea. If we or a companion has good smithing, why shouldn't we be able to "fix" weapons, as you say, removing negative modifiers and/or adding on positive modifiers?
yes this would be a good addition, at least allow us to repair the items, removing negative modifiers
speaking of "repairing" items, I'm experiencing a bug that resets all the modifiers from items in my inventory (sadly it remove the good modifier too), but I don't know how to reproduce it, I simply leave negative modifier items in my inventory and wait till they loose the modifiers, pretending that my men had done the repairs in their spare time