Hi
I have a problem with articles.
they are available at:

mydomain.com/category1/category2/123-title
mydomain.com/123
etc.

Is there a way to block or redirect addresses that are different than those that are at the category page?

Is that item's category mapped into a menu item?

Yes, all categories are in menu.

Then you are 50% there.
In order to never have Google index something you do not want you will canonical links pointing to the URLs generated from these menu items.
Canonical links have the same 'weight' as 301 redirects.

Furthermore, normally mydomain.com/123 would not appear, are you using K2's advanced SEF?