To make things clear AJAX applications have two parts :

1. Server side


2. Client side

Now what the paper is talking about is the client side : playing with DOM, Hijacking JavaScript by inserting malicious code ... but when could this happen ? If a website is vulnerable to XSS ! And to protect your website/application from XSS simply never trust any external data, it's the general rule which is valid for all application development. And when an application is vulnerable to XSS, I don't think we need to give it a new name, because techniques of exploiting XSS bugs are countless.

So we talked about the client side which is vulnerable, but not harmful ! Back to the server-side of the AJAX applications, now if we don't trust any external data, apply correct validations and correct application design, our application will be certainly vulnerable and in this case it could be harmful.

Conclusion

If your application is vulnerable to XSS, it is harmful - AJAX is just the tool which have been always used nothing really new. The only problem I see here is that many developers don't really care about XSS bugs and don't find it harmful, so this will depend on your application and need to do further investigations before making conclusions.