Now that the new database layer supports dynamic runtime alteration of dynamic queries using hook_query_alter(), the time has finally come to exterminate db_rewrite_sql() and replace it with a proper structured approach using an alter hook.
1) Convert all db_rewrite_sql()-using queries to dynamic queries using the new query builder.
2) Tag those queries that should be manipulated by the node access system with "node_access".
3) Write the alter hook to add the necessary joins to do node access stuff.
4) Delete all hook_db_rewrite_sql() code.