I guess we are talking about two different things. I see the Catholic Church as a institution like no other.
The apology should come (if indeed one is forthcoming) from the church as a whole not individuals who have nothing to do with with happened hundreds of years ago.
It is far different then asking for the US gov.org to apoligize for slavery. Comparing the names and nations you mention to the church is far different because all of those have come and go but the Catholic Church has stood "upon the rock" for two thousand years. Like I said it is a institution like no other. If you cannot see that then I will not discuss the issue further. You may have the last word.
EVERY educated and civilized Catholic I know agrees that religious executions and religious-sanctioned murder are wrong. And I am not sure that liberal secular humanists, despite their enthusiasm for pointing figures at odd moments in Catholic history, would find the revival of religious military orders to be all that welcome.