How to hide the reply section of conversation in mail.app?
I'm going to offer a suggestion and a possible workaround (or two)...

First, if I understand your concern properly, what is likely happening is that one of the people involved with the thread has a mail client that isn't properly quoting the content and so the mail app (like gmail before it and numerous other desktop mail clients) doesn't know what is part of the current email reply and what belongs in the past as part of the previous thread of replies. If this is the case, I'm afraid that there's nothing to be done with this current thread to fix it. Perhaps scroll back through the thread and seek the first time this occurred to determine who the offender was (whether they were aware they caused it matters not). Really, all this will do is let you know from whom to expect this in the future. It won't really fix the problem as I believe there isn't a solid solution apart from editing the email on your own prior to your next reply, which I would not recommend because if it happened once it's likely to happen again.

Possible Workaround 1: Send a reply to the thread stating that it's the "Archival Log" and include everything prior to it. Next, Send another reply where you include perhaps only the last 3-5+ replies, whatever holds up the thread to scrutiny re: current discussion. At the bottom of that email, place a text string suggesting to all involved that anything previous can be found in the archival reply making note of the date/time of the archival reply so they can easily search their inbox or saved folders for that thread for reference.

Possible Workaround 2: This might ruffle some feathers, but simply follow the second half of the previous suggestion noting that it's been truncated for simplicity.

Possible Future Workaround 3: This option is only available to those who have autonomy over their systems or when everyone involved has accommodating IT folks and a team willing to move away from email as the primary means of comm for whatever is being discussed... 
Consider moving these types of conversations into a messaging app such as Slack. I started using slack for work about 5 years ago and have since created environments for my family. The reason I prefer it to email is that the whole "reply thread" isn't a thing anymore. Comments flow as they're made. No chance for replies to get crossed "in the mail" when multiple people are drafting their replies at the same time. Slack does have a "threads" feature which does work well for quick branches from the original discussion, but more than a year after it was released, it's still cumbersome to use. If you have multiple tasks or responsibilities being discussed, also consider a free project management task manager such as Asana. The beauty of asana is the ability to maintain threads specific to tasks much better than a plain messaging app. I'm not a fan of their mobile app, so I only use asana within their desktop browser web app. In a pinch, I'll look at the mobile app when away from my desk to see if I need to hurry back to the comment or if it can wait.