Thanks to rachenj who submitted the bug to Show Slow bug tracker, now we have this feature.
Configuring query string pruning is easy, just set $dropQueryStrings = true if you want to drop all query strings or set it to an array of URL prefixes to match.
You can find full documentation on the wiki:
Go ahead and download latest code from trunk:
Have fun and post your suggestions to the mailing list and bug reports to the issue tracker.