I found this thread probably like most of you- trying to fix this extremely annoying pop up thing! Absolutely horrible idea. However, a couple of things..
There has always been a similar feature- the message text used to pop up, but it stayed enclosed in the notification bar. Now that I liked, because if I caught the message as it came in I could read it without even opening the app. Thus far I have found no way to get that back. I have, however, been able to keep the notification of whatsapp while disabling the annoying pop up. Oddly enough, you do it by turning it ON. Set it to show pop ups only if screen is off. Now, if your screen is on, you will only receive a icon in the notification bar along with your normal notification sound. Not sure about the other messaging apps, but it worked for whatsapp.
Hope this helps!