Steven,
Maybe I'm not quite reading your question correctly, but the SQL Server databases are a core, fundamental part of the BizTalk setup. Without them BizTalk would not run; if you were to lose the databases you simply would not have a BizTalk environment.
Furthermore, you need to run the BizTalk backup jobs and not just 'normal' SQL Server backup/maintenance jobs because of the need to add transaction log marks across all of the affected databases. The 'Backup BizTalk Server' job performs this task for you (but it does need to be configured!). More information can be found at: http://msdn2.microsoft.com/en-us/library/ms962212.aspx
In our BizTalk environment, we perform fully daily backups and hourly transaction log backups and keep the files on-site for two days. Anything older is archived to tape and stored off-site.
Hope that helps?
Nick.