Janeway needed to make the Maquis feel respected and useful. Giving them their own uniforms or colors would only have isolated them and made them feel rejected. It helped that Chakotay was on her side, and thus all the Maquis do what he says, but it was in everyone's best interests to make the Maquis feel that they were just as important to the functioning of the ship as the regular Starfleet crew was. The best way to do this was giving them regular uniforms.
The rank pip issue was mainly for the *viewer's* benefit, I think.
The rank pip issue was mainly for the *viewer's* benefit, I think.