To stop disclaimers to appear in replies, just add some random generated string to disclaimer and add exception to that rule. That special string could be the same color as background, so it will be invisible in message body. You can add just some text from the disclaimer to exception condition, but if that text will be in message body then disclaimer will not be added to that message.
To add rule login to exchange admin center, select "mail flow" -> "rules", click "add"->"Apply disclaimers..."
Enter name and condition when disclaimer should be applied, select action "Append disclaimer...", enter text,and at the end add something like "<span style="font-size:10.0pt; color:#FFFFFF">2578AABHKJ213</span>" (there 2578AABHKJ213 random generated string and html tags make text size 10pt and text color is white, so it will be invisible on white background)
Next press "more options..." link, select "add exception if subject or body contains..." and add "2578AABHKJ213"
