In the meantime, there's a decent workaround:
-Turn off the "switch Command and Control keys" option in the SC2 client.
-Go to System Preferences > Keyboard > Modifier Keys
-set "command" to be controlled with the control key, and "control" to be controlled with the command key.
It's obnoxious to have to do this every time you play, but at least you don't have to learn to use control until the issue is fixed.
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