Well, my suggestion is that you should do this work in a branch of openmrs-core, since I think that’s the most straightforward, and least likely to run into other dependencies.
If you’re doing this in a module, I guess that nothing prevents you from dropping a constraint on a table that’s in core, though any core code that references the table may break as a result. And in a module, to change the way that cohorts work you may have to jump through the hoops at the Extending a Table Through a Module wiki page.