> the whole doesn't necessarily have the properties of its constituent parts.
This is because the "constituent parts" - members of the organization - are often just terrible human beings that hide behind the concept of an institution to shield themselves from the cognitive dissonance caused by their own unethical actions.
If an institution does something unethical it can always be traced to its employees.
As an example, all the researchers involved in promoting this fake health product ought to be fired and academically blackballed. It really is that simple. That's how we can deal with institutional rot.
Difference in the parameters. If immoral activity suddenly isn't immoral or rather "okay" if executed by an "institution" how can a (so called) "terror Group" be judged differently? Why are they responsible for the institutional actions while other institutions (or the people behind them) are not?
Yes, but the point being made is that in the case of organizations the whole doesn't necessarily have the properties of its constituent parts.
> If not, what's the difference to any other organisation such as, in an absolute extreme form, an army or a "terror"group apart from the agenda.
Not sure what you mean by this. Difference from what to any other organization and why that relevant?
You find immoral, illegal, etc. activity in institutions/organizations across a broad spectrum of areas.