Limit node.js updates if the view is active
I had and just have the same problem with node.js views update. It seems that the module is refreshing every view that's in use.

I managed to get a workaround by styling my news feed with an open comment section. But i think this is only a solution when you do not expect a hughe amount of comments.

In another use case I implemented another workaround with jQuery:

On my page users can create requests and other users are able to answer these request. A request is a node type and an answer is a node type. They are connected through entity reference module and i wanted to have some sort of inbox functionality where every answer to a specific request is shown in a menu on the specific request page. A user could then click on a answer-menu-item and the whole answer is shown under the request. To give it a more chat feeling I implemented the comment form of the specific answer and styled it to look like a chat form.

This is done with two views implemented on that page. The menu functionality is done with jQuery (Click on menu item -> show related views row of second view). With node.js views refresh I managed to get the chat feeling (When a new comment is added -> refresh first and second view).

I then ran into the same issue like you described above. Each time a user submitted a new comment both views refreshed but the views returned to the their output states - for example: the user was reading an answer of user G and was commenting on that answer when the view was refreshing because of a new comment on an answer of user Y. The view returned to its output state and was not showing any answer because they were initially hidden to achieve the inbox / menu functionality. 

My workaround for that problem is: 

var content = [the views-row belonging to the menu entry]
$(specific-menu-item).click(function(e){
    $(".my-second-view .views-row").hide();
    $(content).show();
    Cookies.set('latest-viewed-answer', content);
    return false;
    e.preventDefault();
});

$(document).ajaxComplete(function() {
  var latest = Cookies.get('latestmessage');
  $(".my-second-view .views-row").hide();
  $(latest).show();
});


To get the Cookie thing working https://github.com/js-cookie/js-cookie

Sorry for my long answer, but i thought that it would be necessary to understand my needs to understand my workaround...

Because this is still a workaround and because I'm asking myself if there will be performance and server issues with our approaches (news feed and chat) I would love to see a solution that is really solving the problem.