In my opinion it should be avoided that objects are really deleted in the Windchill database. Even if a part is not used anymore it shouldn't be deleted in the database. I would prefer a flag on each object that prevents it from being searched and attached to other objects anymore.
The main reason for this is deleting means that there is no further investigation possible -- a deleted object cant't be restored and you can't also find out what was delted and who deleted the object. If you think of an ERP System that would allow deleting objects this would be a desaster.
Feel free to discuss on this issue --- i'm sure ther are other opinions on this as well