There is a conceptual difference between what you are trying to show here. The first is a filtering of all the user resources in the system based on some criteria. The second is showing the user resources that belong to an organisation.
The second url is ok for showing users that belong to an organisation I think.
The first url is effectively filtering the users that you want to see from all users.
Using the url might be ok for the filtering, though using url querystring is also be ok. so
mydomain.com/users?organisationId={orgId}
might be preferable. The urls can still contain querystrings and be restful.
Does it really make any sense to DELETE mydomain.com/users/organisation/{orgid}? Would you expect that to delete the organisation? if not then this isn't really pointing at a resource and so you are doing a search, and should probably use querystrings.
There are other options for doing the search like making the search criteria a first class object, or using one of the other filtering techniques in this question or this question
