No, the government did not stop Michael Cassar from investigating
The government cannot stop or restrict the Police Commissioner from investigating anything. The Police are a separate power to the government. The government can stop the Police Commissioner only be removing him, as it did with John Rizzo, who persisted in investigating John Dalli.
It did not do so in this case, which tells us that the decision not to investigate, and to simply step away from the mess when the pressure TO investigate began to mount, was Cassar’s own. The fact that we are speaking about the government telling the police to do this and the government telling the police not to do that, as though it is entirely normal and the police are an extension of the government, shows how backward we are in failing to understand how institutions function in a democracy, what democracy is (apart from a vote once every five years), and powers are separate and act as a check on each other.
The police have the power to investigate the government, so it should be BLINDINGLY OBVIOUS that the police do not take orders from the government unless they want to, which is an act of abuse and corruption.