Chakotay and the Marquis never become part of Starfleet, nor wear Starfleet uniforms. Chakotay rejects Janeway's insistence on this. They would crew aboard her ship with Janeway as the undisputed captain, but as either foreign military allies, or as "civilian contractors." When Janeway states she can't have two crews, Chakotay reminds her that this is exactly what she's going to have if she wants their help.
I always thought that Janeway has been was too soft and conciliatory with Chakotay.
I don't think so. Whenever he crossed the line - and it was really in "Manuevers" and "Scorpions" - she stomped on him hard.
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