I'm using many 1-TO-1 chats, and on left part of the screen these are listed vertically. Whenever looking for a person, or looking for a specific person which has sent me a message, I sped time looking at the full list. Would be faster to have them ordered by name, without having to move them manually.
While this currently is not available, you can certainly add a comment and vote for it here:
Sort 1-on-1s by recency, first name, etc – Customer Feedback for Flowdock
You may consider closing 1:1s you don't use often to help "clean-up" the clutter. Then when you reopen a closed 1:1 all of your old messages will still be there! I didn't know that for a long time so I kept all messaging open, once I learned that the conversations were saved I closed a bunch and it has helped me tremendously!
Hope this helps!