Hi,
I'm setting up a relatively low cost theater system in a room with an awkward setup.

I'm getting an Onkyo HT-SR800 7.1 Channel receiver w/ speakers.
I need to get a Blu-ray Player with analog outputs to get dts-hd and true-hd formats, but the ones available right now don't have 7.1 outputs. I was thinking about just getting one with 5.1 outputs and running the 2 extra speakers as extra rear speakers given the size/awkward layout of the room.

How would this affect the sound if i have a 5.1 system with 2 Right Rear speakers and 2 left Rear Speakers?
I know I won't be able to get great sound at each sitting area, but what would be best? I'm more interested in getting good sound from the Chairs, not the couch.

This pic shows the proposed 5.1 setups (with 4 rear speakers) with red circles, and a 7.1 setup with Blue circles. The green line is a 73'' mitsubishi dlp. Black boxes are Chairs/couch.
http://img90.imageshack.us/img90/1160/roomsy3.jpg

Is going 5.1 w/ 4 rears OK? Or should I wait for a blu-ray player with 7.1 analog outs?

You're confusing two different things: correct setup of your room/system and the capabilities of your Bluray player.

You should definitely setup your room for 7.1. For the surround left/right speakers, draw a line from your left speaker through your favorite chair and to the right speaker and this line should be parallel to your screen. For the surround-back left/right, your red circles are close, but again, i would make a line parallel to the display. In fact, your red circles look pretty close to a good 7.1 setup for that room.

As for the Bluray issue, you have two options:
1) connect the optical output and use the Onkyo's Dolby PLIIx mode to get 7.1 sound out of 5.1 source - so you'll get all channels, but not the HD sound formats
2) connect the analog out and get the HD formats in 5.1 (should still sound great) - unless the Onkyo is able to apply PLIIx processing to the analog outs, but I doubt that

Experiment with 1 and 2 and see what you like best.