ASP.NET Security Issues with jQuery – How to Ensure Safe Development

Based on the information you provided, I think people can only advice, not provide an architecture:

1. Try to wrap jQuery functionality, specifically ajax part, because you may want to create a centralized place to do something later in your project (for example, to implement client-side redirection to login page on ajax calls, which is commonly known as session management with ajax)
2. Avoid Page Methods and stick with web services. The main purpose of Page Methods is that, they are miniature web services, scoped to the page. But in large applications, sooner or later, you need that method in another page too. Thus, try to use web services as much as you can.
3. One of the biggest problems of large web applications is that, they get bloated with tens of client-side libraries. You need and HTML editor, you add many libraries. You need JavaScript lazy loading, you add libraries. You need unit testing in JavaScript, you add libraries, and so on and so forth. In small projects, people accept to include every library in a master page, even if it's not used in one derived page. However, in large applications, you may come across a point in which, you have 20 js libraries on one page, from which you only use jQuery. You need to address this problem on a regular basis.
4. Another problem I personally have experienced is paths (URLs) to your web services in JavaScript. They can become a headache when you simply reorganize the file system structure of your project as it gets bigger and bigger. I recommend either change to MVC (so to get the URL of actions via Url.Action method), or to just create some kind of PathBuilder utility class to generate the URL of a web service based on some parameters.

Server architecture seems to not being touched that much with larger projects.

It sounds like you're struggling with :

• Maintaining a "rich" UI
• Doing most of your interactions via AJAX to the controller
• Keeping the front-end in sync with results of AJAX actions

If I've understood your issue correctly, you may want want to check out KnockoutJS, which is a javascript framework built for handling just these kind of scenarios. Take yourself through the interactive tutorial examples, it'll build the concepts you need slowly and logically. Quite a nice framework.