Any company that sells this type of services exists as an extension of its parent state. Any contract it offers, especially to a political entity in another state, will be scrutinized by state authorities and allowed by them or not. Sometimes, those contracts will be forced on the company based on state-level negotiations.
Noone is saying that the party that contracted this company (if indeed it was a Slovenian party and not the Israeli state itself) for this service doesn't carry blame. But both the company itself and the state of Israel carry just as much blame for offering, permitting, and carrying out such services.
By your logic, if someone were to found a legal private paid assassin company in France, and then the opposition party in Germany hired this company to assassinate the German chancellor, you'd say that it's unfair for Germany to blame France for this.