It would make more sense, to me at least, to build a mail service from the ground up than to try to manipulate an open source MTA to alter the body of an email in transit.
I agree with you, but it's not only company's that do that, also government's are using this method if I'm not mistaken.
I worked at a regional government, which was using Exchange. They needed, being governmental, such disclaimer to prevent being held responsible from certain statements from employees, which shouldn't do these statements in mail.
That is a very good and valid reason to do something like this. So somehow, as far as I know, they created some way in Exchange to add this text to every outgoing mail. This way the users weren't able to change this "signature" if they would by accident get config rights on their outlook.
So indeed I agree MTA's shouldn't be manipulated for this. On the other hand, since multiple company's and governments have a valid reason for adding a disclaimer, it might be good for MTA's to create something like this as an addon or something.
Just because almost everybody uses existing mail clients and won't start building things from scratch to achieve something like this.
I'm not that big into mail as you, but I wouldn't know how to achieve this in another way.