To begin with, the problem is that people only pick out a part of the entire system, instead of looking at it as a whole. Take for example, the eye as a whole is a beautiful and an amazing creation, but in pieces it looks abhorrent. So if I look at bits and pieces of the religion and based them on my prejudiced thought it won’t align.
Islam isn’t about cutting a thieves hand or killing an apostate, this is what the unbeliever wants to bring out in order to attack the religion.
This is only acceptable with a full functioning Islamic System.
Another thing, if there is no punishment, then there is no security, the classic paradox, without law and order, man has no freedom.
As for the jurisdiction of Islam, no country’s government is limited to their borders. If the sovereignty of any nation is breached they will cross borders to defend their rights.