Yes, I ended up adding code to not start the streaming until told to, but once the streaming starts, it still causes undesirable behavior on the computer side of things -- the serial port is "unavailable" most of the time, at the OS level. I can't help but think that this means that the 8u2 on the Arduino Uno needs some smarter code on it, but I haven't had a chance to verify how FTDI Arduinos function in this situation. Maybe they suffer from the same "limitation."
As a naive user, I would expect the port to always be available regardless of whether the uC was streaming serial data or not.
In any case, the IDE shouldn't hang for so long looking for ports every time the "Tools" menu is clicked.