I don't want to go to other app for that, so electrum and it's 1000 limit for one wallet is not enough for me. Simply it is blocking IP addresses with larger wallets.
1. It's not IP block, but rate limit to prevent DDoS.
2. You could setup your own Electrum server and remove the rate limit.
But since Electrum wallet doesn't scale well (one of the reason it use JSON structure), i think you'll need to tweak your script to create new wallet after every X private key imported.