Existing super mutants are not necessarily just looking to kill humans, but they are territorial and wish to survive and thrive.
Many were created and released by the early Institute and BIO science department to see is they could survive. As intelligence varies with super mutants, those smart enough eventually establish their own settlements, such as Breakheart Banks, and have long term plans of their own. Even though average intelligence of those first super mutants wasn't what the designers were seeking, leaders like Strong and those smarter than the average super mutant could easily go on to start building up their own race.
Half super mutant offspring were found from time to time, proving that these genetically altered humans could reproduce on their own. Females and offspring were never seen though, as they were obviously hidden and protected at all costs as this fledgling race established itself. These superior mutants wouldn't want a constant war though, and may be willing to trade, work together, or even become allies with other groups to ensure the continuation of their race.
Breakheart Banks should be a recruit-able location like other settlements.