Digging around on the web, a lot of sites seem to lead to two things:
- Marina either defected from the Octoling society, or liked the Inkling better, and decided to stay there. A GameFAQ post discusses this a bit.
- The Sunken Scrolls in Splatoon 2, specifically, the second scroll which depicts the final battle in Hero Mode between Agent 3 and DJ Octavio (explanation below).
The first bullet for the most part speaks for itself, but I think the second bullet is more appropriate and I'll attempt to explain my thoughts. The in game description for this scroll states:
Music heads are still buzzing over that legendary underground show two years ago. Anyone lucky enough to catch DJ Octavio's opening set and the Squid Sisters headlining had their minds blown and their lives changed that night.
The scroll can be seen below:
Circled in the picture, is Marina, which is also noted on the Scrolls Wiki page as well as on Marina's page. Marina was apparently present for the battle between Agent 3 and DJ Octavio. Considering the above description for this scroll which states " Anyone lucky enough to catch DJ Octavio's opening set and the Squid Sisters headlining had their minds blown and their lives changed that night," I think Marina's life changed after this event, and she decided to join the Inkling society.