OK, I still dont know what is ContentItem and ContentItemType used for, but I managed to delete ContentType using umbraco API functions.
The trick is actually that I was supposed to use DocumentType class and its method delete() instead of ContentType or ContentItemType classes.The actual code that might help you if you have the ID of Document Type you want to delete, looks like this:
Code:ContentType contentType = ContentType.GetContentType(YOURDOCUMENTTYPE.Id);
DocumentType dt = DocumentType.GetByAlias(contentType.Alias);
dt.delete();
Hope this helps someone..