Not that I'm sympathetic to the decision to fire here based on what I know (which is really just this article and what I've read in this thread), but the two issues seem to be somewhat orthogonal, in that I could imagine a consistent moral framework falling either way with different opinions on them. Someone might believe in the importance of minimising consequences for speech on a public forum such as Twitter (whose end purpose is supposedly such speech, and which is one of the main venues in which public political discourse in fact happens), while simultaneously not believing that employees of a company have the right to speak up against the interests of that company (whose purpose is making widgets and money) and be protected from the company terminating the working relationship in return. Conversely, someone might think of unfettered political debate as harmful, and believe in the importance of suppressing certain opinions they find dangerous and harmful from the public sphere, while also believing that letting employees criticise and organise against their employer is important to guarantee the welfare of employees and keep the power of employers in check. In fact, the two combinations seem respectively pretty close to the proclaimed ethos of the US and the Soviet Union respectively a century ago.

Criticism of Musk's action here may come both from those who in fact are in the "free speech absolutist" camp and want both the Twitter deplorables and the corporate gadflies to be protected from retaliation, and from those who are just in the latter position and want the opposite pattern, but I think only the first group can bring a charge of hypocrisy (still incorrect, as it ignores the orthogonality) without it making themselves guilty of higher-order hypocrisy.