I shopped and compared these two bikes a couple of months ago and here's what I concluded.
I would choose the Muir woods based on these comparisons:
The Muir woods has a chromly frame which is a better ride vs. aluminum.
I would prefer the simplicity of V-brakes on the muir woods rather the disk on the Novato.
The component comparison is not as drastic as the salesman made it out to be.
Look at the build where is really matters ( drivetrain , wheels, brakes, frame material)
Start with a good basic bike and build up from there.
And finally, ride them both and see which one is right for you.