I had the same problem and found this thread while looking for a solution. I had way too much disk space taken up with messages so I tried to create some room by deleting whole conversations using the edit button on the main screen. The conversations would be deleted, but then the Messages app would slow down tremendously (almost freeze) and I would lose the ability to scroll back through the conversations that I had kept. After a restart (of the app or the phone), the messages/conversations I had deleted would reappear and the app would run smooth again.
After some experimentation, I resolved the issue (at least on my phone).
Try to delete the conversations as you would normally, but allow your phone to sit without using the Messages app for a few minutes (it will be slow/frozen if you do anyway). After a few minutes, the app will return to normal speed and functioning. The period of time before the app returns to normal will vary depending on the number of messages that you are deleting. When a conversation is deleted, I believe the Messages app continues working in the background to actually delete and reindex the data (thus slowing down its normal functioning). I am suggesting that this is the case because after deleting many conversations and freezing up my Messages app, I went to Settings-->General-->Usage and watched the data that was used by the Messages app drop repeatedly over time as it worked in the background (you may have to refresh the usage data by exiting/reloading the window). For reference, I deleted about 1.2GB worth of messages and watched the data continued to drop for about 5 minutes before it stopped. After being patient and waiting for the data to stabilize, I was able to use the Messages app normally again. I restarted the phone and the deleted conversations never reappeared. Try it out. And remember to backup your phone prior to doing anything involving the "delete" functions--just in case!