You seem to have covered the situation pretty well. Transcode in Final Cut, works great. Work native in Premiere, doesn't work so good. Want it to work better, use a lower bitrate. That seems to sum up the current reality of AVCHD editing.
If I go to a lower bit rate, how much will the effect end quality?
The point of having a camera that records in a higher bit rate is to use that bit rate. The update for CS4 at the end of the month, will that address any of these issues?
You're the one with the camera. I suggest some tests - shoot the same few scenes at various bitrates and watch them directly on a properly calibrated HDTV. This will give you some direct observations about quality differences between bitrates.
My own viewpoint is that there really is no point to any camera using GOP compression. It's just a bad idea from the start, so if one has issues using such a camera, I see that as "caveat emptor" situation.
I'm not aware of any official announcement from Adobe on the full list of what will be updated/corrected/fixed with 4.1, but my guess (and it is purely a guess) would be no. I'm inclined to believe this is primarily a horsepower problem.
In CS4 try exporting the high bit rate AVCHD as MPEG2 1440 X 1080i, 1.33 pixels, high quality. Import the new files to an HDV sequence and edit there.
If you can convert to prores in FCP then you should be able to use those files in PPro too (assuming both programs are on the same mac).
If you want another intermediate files solution I suggest looking into Cineform. "NeoHD" would be the product you're looking for. The quality would be as good as Prores but smaller files, and you can do color correction etc. in the file metadata using their "First light" plugin (meaning no rendering necessary in PPro). They have promised to release an update to make their video files playable in PPro CS4 sometime this month.