Unhappy client methods, such as the conditional comments used, do not mix with server-side technologies. I believe that the only way to do this with the ScriptManager is to programmatically add scripts to the page if your condition is met.
If you care more about running the script and then delivering it, you can do something like this:
And then, in your script, wrap it with if (typeof (isLteIe8)! == 'undefined') {...}
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