Well, if you're willing to start a new fort, you could go through the raws and simply delete all forms of non-armor clothing (including, or only, removing them from all entities' allowed items lists). That'll save you a large number of items on the map as well as reducing the number of things that appear when goblins do. Reducing the number of items goblins bring by eliminating most of their useless clothing will also save hauling efforts.
Also, you could, rather than sending out your soldiers to take the goblins wherever they appear, have your soldiers lie in wait someplace closer to your fort, preferably at a choke-point of sorts. This will make all of your kills be in the same general area, and then you can drag them to an atom-smasher more easily. In addition, try to use piercing or blunt weapons instead of slashing, as they'll dismember your enemies less and create fewer body parts.
Um. Other stuff to do... You may, for your future forts, want to look into the Intensifying Mod, which consolidates many body parts that may be considered irrelevant, such as fingers, toes, and teeth, as well as those that have redundant or no functionality into single pieces. For instance, it turns all the teeth into a single "jaw" body part. Reducing the number of body parts in this fashion is believed to improve FPS as the eliminated body parts don't need to be tracked as much.
The Fortress Defense mod also has some enemies, "supernatural" ones in particular, drop a particular type of custom stone on death instead of a corpse. That stone immediately evaporates, so those creatures essentially don't leave corpses. Something like that would also reduce your clutter with each ambush.
Probably your best bet, however, is to simply get used to playing at lower FPS. Most people consider the game "playable" down to ~20 FPS, with 50-70 being good. Since your fort will usually not require your direct attention at all times, it's fine to have the game running in another window while you do something else, only checking every few minutes back to make sure nothing pressing needs your intervention.