This is currently not possible by default and last time I checked only somewhat supported by the underlying library. You can set a separate html body in code though, on the ExchangeEmailDTO class used in EmailSaveAsDraftOrSend, so if you are comfortable in Java you could create this. However it may be hard to have to deal with both a regular body and html body. Best option is upgrading the relevant Exchange server to 2007 or up and using the module for that version.
Well all you need to do to change that is, instead of getting your from address from your settings object getting it from the designated user. That should not be to hard to change, in fact if it is based on the current user all you need to do is build an extra microflow that casts current user to an account or any other type of system.user that has an email account and return the email adress as the from address.