Apple Mail isn't going to change the format of any of your attachments. it isn't going to corrupt them either.
Exchange is a transport protocol and server. The issue you describe is not related to Exchange.
There are many different versions of Microsoft Outlook in use and they all have e-mail bugs. Different versions have different bugs. Some Apple Mail hack to get around a bug in Outlook 2003 may cause the same message to be problematic in Outlook 2000. Fix them both and another issue will cause trouble in Outlook 2007. You can't fix this. Apple can't fix this. Microsoft can and has but that is irrelevant if your recipients are using older versions.
One specific problem is that Apple Mail always sends image attachments inline, as images, not as iconized files. You can change this with Attachment Tamer. Just be aware that use of this software will break other things such as Stationery. E-mail is just a disaster. To date, no one outside of Apple has ever implemented the e-mail standards from 1993. Apple has continually changed its e-mail software to be more compatible with the de-facto standards that Netscape and Microsoft have unilaterally defined and people documented as "standards" after the fact. The e-mail messages that Apple Mail sends are 100% correct and do not violate any of the original standards from 1993 or the Microsoft/Netscape modifications. The problem is entirely bugs and limitations in various versions of Outlook.