The fact that you will be using a 2 channel preamp downstream of the processor is exactly my point. Many of the top BD/DVD/Universal players have very good internal Dolby TrueHD/DTS Master Audio/Dolby Digital/etc processors built in so that you can come straight out of their analog outputs to your preamp when listening to 2 channel Dolby/DTS encoded lossless BD/DVD's (hopefully there will be more of those in the future) or SACD/DVD Audio. This eliminates the processor (and it's non-defeatable analog section) from the signal chain for serious 2 channel listening.
Regarding eliminating the video inputs on HT, I think you will find that the whole multi-channel HD signal chain (source -> processor -> display device/amplifiers) is built around HDMI which automatically incorporates video, so your concern is somewhat academic. As Kal points out, the advantages of running video through your processor (switching, video picture adjustability) outweigh whatever small negatives that concern you.
For example, when I am watching HD sources, I set my processor's video setting to "Through" (bypass), but I engage the internal Reon video processing on non-HD sources to reduce video artifacts (clean up the picture).