This is something the causes a lot of frustration. In our case, we have a company with more than 500 people. So it's hard to remember or find only in the notifications bar the people which you talked with. From time to time the notification also disappears and you can totally miss someone's chat because you, for example, forget its name.
As you know, it is currently a manual sort for 1-1's. Here is the Feature Request on the Flowdock Uservoice page for what you are requesting:
Sort 1-on-1s by recency, first name, etc – Customer Feedback for Flowdock
You may add your vote and comments to that request to gain more visibility.