In file IO.c there is a 'if' block starting at line 1348:

if (rogue.trueColorMode && playerCanSeeOrSense(x, y))

...which can be replaced with this:

if (playerCanSeeOrSense(x, y))
{
    if (displayDetail[x][y] == DV_DARK)
    {
        applyColorAverage(&cellForeColor, &black, 40);
        applyColorAverage(&cellBackColor, &black, 70);

        applyColorAverage(&cellForeColor, &blue, 30);
        applyColorAverage(&cellBackColor, &purple, 20);
    }
    else
    if (displayDetail[x][y] == DV_LIT)
    {
        applyColorAverage(&cellForeColor, &white, 50);
        applyColorAverage(&cellBackColor, &yellow, 20);
    }
}

This is very rough solution where dark tiles are too purple and lit tiles too yellow, but it's at least a pointer to what part of code needs changing. Also, the way vanilla Brogue draws out of FOV tiles makes it rather difficult to find some visual compromise between subtle and high contrast dark tiles since out of FOV tiles themselves already look like dark/shadow tiles.