Is there a word with a meaning in between 'desegregate' and 'integrate'?

Solution 1:

How about unintegrated? From Cambridge:

integrate: to mix with and join society or a group of people, often changing to suit their way of life, habits, and customs

Based on this, integrated implies mixing with and joining society or a group of people, often changing to suit their way of life, habits, and customs. By the same token, unintegrated implies not mixing with and joining society or a group of people, often changing to suit their way of life, habits, and customs.

Your example:

Although not segregated, they did not dwell together in unity preferring to be (remain) unintegrated.

One could be against segregation -- that is, one could be for desegregation -- without being in favor of or engaging in integration. Thus speaks Pudsey.