From your logic Israel should have booted the Irish ambassador for Ireland allowing the SS pancake to sail from Ireland
Israel is a sovereign nation, it certainly may expel the Irish ambassador if it feels that is in its best interests. The Irish haven't broken the law, it is not illegal to run a blockade under the San Remo Manual... stupid maybe, but not illegal. Your point about the SS Saint Pancake is irrelevant, however, since the Irish government has already authorized the IDF to board the ship. IT would be pretty stupid to expel the Irish ambassador for that.
However, that issue of the SS Saint Pancake really has nothing to do with Israel illegally forging Irish passports and assassinating people while using them. Ireland hasn't done anything like that to Israel to infringe on Israel's sovereignty, and Ireland, so far as I am aware, hasn't yet assassinated anyone on a forged Israeli passport.