We have set and retrieved the spinnakers out of and into our rigid carbon spinnaker "chutes" on the F14's hundreds of times and there is no sign of the type of wear that you describe, In fact one spinnaker is getting towards the end of it's "racing" life now and the only wear showing is in the "shape" of the material through loading "stretch" and age. If the "chute", the halyard, and the retrieval line are all set up correctly, there shouldn't be any untoward wear, regardless of which ever side the kite is set or retrieved.
We use a continuous halyard/retrieval sheet line running through a 2 to 2 pull out to the end of the pole and both the set and the drop is "lightning" fast.