Run it like this:
importprivkey "" false
That will import without rescanning. You'll probably have to restart with -reindex afterwards, so it finds the relevant transactions, but at least it'll only do it once.
If you run the first 99 imports with the "false" flag, then those 9 keys will import without scanning the blockchain for transactions. The balance won't update to reflect any bitcoins that are accessible with those 99 keys, but the import will complete very quickly.
Then when you import the 100th key, leave the "false" flag off the import command. After importing the key, the wallet should scan the entire blockchain just once and find all the transactions associated with all 100 imported keys. The balance will reflect all bitcoins from all imported keys.
If you find that the balance isn't correct after the imports, you can force the wallet to scan the blockchain with a -rescan command line option.