On a load-balanced (2008R2) farm of two servers, is there a way to force a user's logon to a specific server or to force one app to launch on a specific server instead of being assigned by connection broker?
Yes. You can create a .rdp connection file with the IP of the specific server you want the user to log into and save it on the user's desktop, the cons of this workaround is that you can't manage it from a centralized location but it will allow you to force a user to connect to a specific server.
Another thing you can do, is to create a shortcut to the application you want the user to use, you do it from the mstsc window itself, under Programs tab:
In that way, you can place a shortcut of the application on the user's desktop and when he'll click it it will open an rdp session to the specified server and lunch the application without giving the user access to the desktop, just to the application.