1. I have had some luck just deleting the PACKAGE component altogether, but others have not. If you do still have just your plain AutoCAD 2008 license appended, that alone will work without the new 2009 stuff added. However, if you do add the 2009 Subscription license to your NLM, then it will supercede any and all 2006, 2007, and 2008 licenses that you may have appended in there also. That is just the way it works this time around. Therefore, if you are only using 2008 licenses and are not using 2009 yet, then I would remove the entire PACKAGE and ACAD_F Increments altogether. This will allow you to run your older working 2008 licenses in the mean-time.
2. It is very possible that your EXCLUDE on the 2008 feature is being ignored because the user is likely on the ACAD_F feature that is pulling the old 2008 license on roll-back. I can't confirm that this is how it works without testing it myself, but it seems likely. This is especially true given that the 2009 license simply makes the NLM ignore your 2008 features. If I had to guess, this is what I would imagine is going on. Furthermore, you are right in the fact that the PLIST of the Suite will pull a vanilla ACAD license if they are available because ACAD is cheaper than Revit. If simply removing the 2009 PACKAGE and INCREMENT do not solve this problem, you may actually have to yank the PLIST feature as well to avoid the cascading.
If I wasn't so busy today, I'd test this with my NLM and 2008-2009 licenses and adskflex.opt.
Good Luck!