Best Pre-Amp w/Throughput for HT ?

If you want the best preamp for 2-channel music listening, then buy the 2-channel pre that sounds the best to YOU in YOUR system. I personally recommend Conrad Johnson Premier 14 or CAT.

Whatever pre you decide on does not need a pass through to work for HT. Just connect the left and right front outputs from your MC-1 to any input on the new preamp, calibrate the system for HT use with the preamp set at a repeatable volume setting (a numerical display makes this easier). When you watch a movie set the volume on the preamp to the setting used during calibration, and use the MC-1 to control the system volume. When doing the 2-channel thing the new preamp controls the system

This is how I configure my system (for HT the CJ is set at 72, which happens to be its “unity gain settiing), and it works great. I can see how a pass thru would be slightly more convenient for HT use. But for you, and me this will limit your choices with regard to preamp. If the pre you like BEST happens to have a pass through then you get the convenience; if not then make your choice for the best 2-channel sound.

Depending on how much you want to spend and if you want a tubed pre or solid state pre, I would consider at least listening to the SOnic Frontiers Line series or the Adcom GFP 750. They both have a HT bypass loop and work very well in 2-channel mode as well. I tried the whole calibration thing with a pre amp that didn't have the processor loop and I didn't like the fact that I couldn't control the volume of my theater in variations. Meaning, that if I wanted to hear the movie but at a lower volume inwhich I originally had it calibrated to, I would have to recalibrate my system just to turn it down to a lower level. I believe that Proceed and EAD makes some nice pre - pros that you might find used and at a fine price and possibly may give you the performance that you're looking for in a one box unit as well.

Good Luck.

With the gear that you have now, I would give strong consideration to either the Mark Levinson 380 or 380S, both have the home theater bypass... go with the "S" version if you can swing it.
Alternately the Krell KRC-3 also has an HT blow-through circuit.
My first choice would be for the 380S.