Thinking a bit more about this, I think that's the wrong key, we need to change the private key of the server. Rclone normally generates an RSA key (cached here ~/.cache/rclone/serve-sftp/id_rsa) however you can set this with
--key stringArray SSH private host key file (Can be multi-valued, leave blank to auto generate)
So you could try creating a ecdsa key pair for the server
ssh-keygen -t ECDSA -f id_ecdsa
rclone serve -vv sftp --key id_ecdsa .
This seemed to work in my tests provoking an ECDSA key exchange.
Probably what rclone should do is generate an ECDSA key as well as an rsa key and load them both.
I'm not sure I fully understand the problem