Stereo Preamp suggestion

op

"Since the AVR is the only source for both music and movies, subs are on when the AVR is on".

yes, IF there is 'surround coding' for sub channel information; but, for 2 channel music, there is no decoding, there is no sub signal for them to work with, which means, they are NOT on for 2 channel music via AVR.

Preamp with HT Bypass would be engaged ONLY during Video, so yes, the front could thus be PASSED to the existing 2 channel amp, wired ONLY to the fl and fr.

btw, there is no center channel signal in 2 channel mode which makes it critical for the fl and fr speakers to create a 'wide' center image for off-center listeners of 2 channel music.

This may help.    

http://www.audiophile.no/en/articles-tests-reviews/item/426-amplifiers-with-processor-input

I was in exactly the same situation a couple of years ago and the solution is easy and extremely satisfying sonically.    
Adding a preamp with HT bypass will be a significant improvement, as it removes the Marantz's preamp from the system. Although you do not provide any source information, I assume you use either vinyl, CD or digital of some sort, so all 2-channel will run through the preamp. If you were to buy the Parasound Halo P6 it would solve a lot of what you are looking for. It not only has HT bypass and dual sub outs, it also has a set of additional sub outs with variable low pass filter and a variable high pass filter for the main outs. 

Mcintosh has “passthru” on many of their preamp‘s. I’ve owned the C1000 and the C8. Both of work flawlessly

A budget number would be helpful.  I used a Modwright LS100 until recently and have since upgraded to a Herron VTSP-360 Reference.  Both have HTBP. 

My subs are active for both stereo listening and home theater.  Many preamps have more than one set of outputs.  You will give up the subwoofer correction from your AVR, but if you run enough subs (I have 4, 5 for HT), it won't matter.