Is Exchange protected from/allow back dated emails?

I am not sure that this really answers your question, but looking at the MSDN reference for the MailItem, and it's time properties may give you an idea what you can trust.

MailItem

• http://msdn.microsoft.com/en-us/library/aa210946(office.11).aspx

MailItem.CreationTime

• Returns a Date indicating the creation time for the Outlook item
• Read-only.
• http://msdn.microsoft.com/en-us/library/aa211817(office.11).aspx

MailItem.LastModificationTime

• Returns a Date specifying the date and time that the Microsoft Outlook item was last modified.
• Read-only.
• http://msdn.microsoft.com/en-us/library/aa171467(office.11).aspx

MailItem.ReceivedTime

• Returns or sets a Date indicating the date and time at which the mail message, meeting item, or post was received.
• Read/write for the MeetingItem object; read-only for the MailItem and PostItem objects.
• http://msdn.microsoft.com/en-us/library/aa171873(office.11).aspx

Is there any kind of "sequence number" that we could use to audit Exchange records for evidence of date manipulation.

I don't believe so. If you really need to audit at this level you may just need to keep a seperate copy of each message/item. Or perhaps you need to come up with a good backup/restore method. If you suspect something check out an older version of the persons mailbox from your archives.