There is not a way to currently do this and have DTM not lose any functionality. Note: We strongly recommend against the method you are describing in your original question.
For now this is a governance & process issue. This sounds like the makings of a good feature request where what you need is the ability to create new user groups with sub levels of access within a single property. The best course of action would be to type this up and send the email to your account manager with instructions to fwd it to the myself or the DTM team.
Generally speaking it is a bad idea to have 2 copies of the DTM engine on a single domain. That would cause conflicts within the DOM of the page and DTM could not be guaranteed to work as expected.
To manage the user roles across different properties ( https://microsite.omniture.com/t2/help/en_US/dtm/#Invite_a_user ) You would select the "Define Role per Property" setting in DTM next to the user name. If you do not provide a user with any access to specific property within DTM then they will not even see the property listed in their dashboard.