if you disable system restore ad re enable it then yes all your restore points will be gone apart from a checkpoint that is created when re enabled.
"hundreds of restore points" really? this will take up quite a bit of your disc space.
do you have service pk 1 installed? i had similar problems with restore not working before i installed it. click here
to remove all traces of the program use add/remove programs then delete any folders left behind in program files or wherever you installed it to.
next click start/run type rededit click ok.click my computer and then back it up by clicking file/export and save to a folder of your choosing.
next click edit/find type the name of the program or developer into the find box and click find next.
it will stop and highlight anything found,right click and delete ONLY THOSE YOU ARE SURE ARE RELATED TO THE PROGRAM IN QUESTION.
tap F3 to contine searching deleting untill it says finished searching through the registry.
restart the computer.