You should only have to re-initialize the entire subscription if, for some reason, it is marked for re-initialization. That could be because of an extended period during which transactions can't be sent to the subscriber. I can't think of any other reason, unless you want to do it. You can drop and add articles without re-initializing and make schema changes.

In SQL Server 2008, in the article properties, you can choose not to replicate delete statements. We don't have a SQL Server 2005 publisher, but I imagine it is probably the same.