Is there some way to prevent these proxy tools from editing the content the user sends to the application?
According to the OWASP FAQ:
"The main threat these proxy tools pose is editing the information sent from the client to the server. One way to prevent it is to sign the message sent from the client with a Java Applet downloaded onto the client machine. Since the applet we developed will be the one validating the certificate and not the browser, a proxy tool will not be able to get in between the client and the server with a fake certificate. The applet will reject the fake certificate. The public key of this certificate can then be used to digitally sign each message sent between the client and the server. An attacker would then have to replace the embedded certificate in the applet with a fake certificate to succeed - that raises the barrier for the attacker."