Just a few thoughts I've got on this.
Certainly people are coming up with some really great JS solutions that are much wanted and make use of new concepts and ideas within Moodle and these are requiring changes in pages in order to possible.
I've been playing a bit with course editing and at the moment while I can see a visible jump I don't find it overly aggressive. For sure if we could avoid it, or minimise it that would be great.
In regards to the suggestions made above.
2. Adding a CSS class to the body is ajax is enabled for the site I think is an entirely worthwhile endeavor. Even if it doesn't form part of the solution for this issue I think that is a valuable idea. Again as more and more JS arrives that is the sort of thing that implementing now will save countless varying solutions to the same problem from occurring in the future. This of course by itself doesn't constitute a solution, simply hiding things only gets us half way there at the moment as presently we have all things shifting in the page when JS loads.
As for the complete solution as hinted at above I think we need to look at the design of the page when in editing mode. Especially the icons and placement of them.
Ideally I think we should stick to the principle of enhancement and try to organise things in such a way that they meet the needs of both the conventional page and the AJAX page.
Most of the JS that exists for editing has been revisited in the past couple of months and tidied up greatly.
Certainly it is more possible now than it has been in the past to look at the design; more needed as well of course.
When I say design by the way I mean where the icons are placed, the HTML that is holding them in place, their size and order, and perhaps even the icons themselves.
In reflection to my opening statement I think we need to change the page to meet the needs of the JS (as well as the conventional page) and not have the JS make changes to the page (unless absolutely required).
Anyway I think that about sums up my thoughts on the concept of this issue. I know that it doesn't provide any specific direction but hopefully it gives an insight into what I see as the direction this issue should be taken in finding a solution.