It certainly sounds hypocritical if you're willing to play liberties with the definition of free speech. However, free speech doesn't mean freedom from consequences of such speech. The audience can respond any way they like without infringing on the speaker's rights (and it's not a right to work at SpaceX).

These employees should have expected this reaction; Musk doesn't seem like the type to pass up executing his right to impose consequences. Hopefully they were prepared and have achieved some of the impact they were hoping for.