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]
var latest = Cookies.get('latestmessage');
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.