It's okay to delete from the tables. There are even stored procedures in MSDB that will do it - sp_dump_dtspackagelog and sp_dump_dtssteplog, though your idea of keeping them for x days will require checking the logdate column.
Microsoft is locking down system tables in SQL 2005, so these might not be available for updating in that release. Come to think of it, they might not even exist with these names since DTS will become SSIS.
Greg