Here is a huge list of presumably legit distributors:

http://arduino.cc/en/Main/Buy

For example: DigiKey has thousands of the Arduino Uno in stock.

Except that there are reports (http://forum.arduino.cc/index.php?topic=307397.0) that the boards from official distributors are shipping with Arduino Srl's USB Vendor ID, indicating that purchasing any "official" Arduino is likely funding the attack on Arduino LLC.

Hence the GP's observation that buying a 'no-name' clone seems to currently be the least-harmful option available.

Except that almost all the boards are sold out. Is there any other alternative?

Sparkfun's Arduino-like boards pay back a percentage to the inventors.