You can put a buffer between your farms and the ME system and use something like Steve's Factory Manager to transfer the items over. Other mods have "fuzzy" item filters to ignore damage values, but SFM allows you to set the filter without even having a sample at hand and has nigh unlimited filter slots in a single block.
Another solution would be to use external storage solutions with excess-voiding upgrades like barrels or drawers. With the controller an entire drawer bank uses only 1 channel on your network and you can still use the priority system to void all excess, but this is only suited to stackable drops.
You can also export the offending items from your system automatically, the "fuzzy card" will make ME buses ignore damage values. Wastes a ton of channels though.
As a side note, if you care to set it up, you can use a Thaumic Restorer (from Thaumic Tinkerer) to repair damaged weapons and armour, then melt them down in a smeltery, blast furnace or arc furnace (metals only, and not all items are compatible with all smelters, check the recipes in NEI). You can get Instrumentum essentia from MFR rubber which even acts as a furnace fuel too, which makes the mobtrap a nice renewable source of gold and steel.