First, you do not have to save selenium IDE scripts as webdriver, you can also save them as RC code. Although I am not sure if that will solve the problems you have. Just wanted to point out that it's not webdriver only.
I do not usually use the IDE, but hopefully this is some information that will get you closer to solving your problem.
If you download the selenium server jar from
http://docs.seleniumhq.org/download/ you can then call that from the command line, pass the htmlSuite parameter and the necessary information for the test suite created in IDE to be run.
Export your test suite as an html file from the IDE (or hand create it yourself) and then run a command such as:
java -jar selenium-server-standalone-2.31.0.jar -port 4444 -htmlSuite *firefox "{{your beginning url}}" "{{path to the test suite html file}}l" "{{path to a results html file that it will use"
You could wrap that up in a batch file.