“Aren’t we commanded to wipe them out? “
Descendents of Haman taught Torah in Bnei Brak. Would you have rushed up to the Rosh Yeshiva and stabbed him to death?
And had the Jews during Bar Kochba worshiped Jupiter, they also would have not been wiped out. Not sure of your point.
Cromwell had a job, and he very possibly did it sustaining the fewest overall casualties. Assuming that you can agree with the cause (overthrow of the monarchy), then he may have done the right thing. If you disagree with the cause, and think the Irish were right in suppoting the monarchy, then no justification can be made.
It just depends on which side you are sitting when you look at it.