well, Janeway also made decisions for her crew that she had no business making. She stranded them in the DQ. If she really believed in helping the Ocampa, she could have let her crew go home, then stayed behind to set the explosives on the array.
The Maquis were drafted, if you remember. They didn't sign on to be members of her crew, so she should have shown greater flexibility in making decisions involving them, since unlike her Starfleet crew, they weren't even there even somewhat voluntarily.
From their perspective, Janeway stranded them and then drafted them.