Normally, yes, it is highly unusual for a Sovereign Power's military force to make an operational decision without the knowledge of the Government and/or Head Of Government.
Israeli Basic Law asserts:
"Article 2: Subordination to the Civilian Authorities,” reads: (a) “The Army is Subject to the Authority of the Government,” and (b) “The Minister in charge of the Army on behalf of the Government is the Minister of Defence.”
Rule 40 a makes it clear only the Government can declare war, but rule 40 b has some ambiguity in that some operational decisions don't necessarily need the authorisation of the PM or Minister of Defence. This may explain the above if that actually happened.
Israel has a structure of Government that's quite different to what we might be used to.
In general, the Israeli Government is in charge of the broader strategic decisions and Minister of Defence is in charge of day to day operations. Israel has three decision making forums - government, security cabinet, and war cabinet.