You can assign users to a class of service that does not have the Text to Speech feature turned on - then emails will not be presented over the phone interface - just voice messages and faxes and receipts.
Not sure I understand your second item - Outlook just being open shouldn't have any effect unless you have some client side rule that's moving messages to a folder or something - unless I'm not understanding your scenario. If you're opening messages in Outlook and marking them read then Unity is going to turn the MWI off - it's based on the read/unread status of the message, which client does the toggling is not relevant.
