The old version can do this. Now the node div uses style visibility instead of display. As we know visibility would use the space even it's set to hidden while display:none will absolutely take out the space.

I have solution but can't commit the changes.

Could you write the changes here or are they too extensive?
It would be great if display or visibility toggle would be an option...

I'll accept a pull request that gives an option to ignores/respects whitespace left by collapsed nodes :) For now here's the version that will collapse into whitespace left by collapsed nodes.

https://github.com/wesnolte/jOrgChart/tree/9763085df24d0507636100e7919d6530391e62c6

I had the same requirement and fixed it in this way:

Changed all occurences of .css('visibility', 'hidden') to .addClass('row-hidden')
Also changed .css('visibility', '') to .removeClass('row-hidden')

Added this to the LESS file:

.row-hidden{
    //visibility:hidden;  //the original setting - use this to maintain the layout on open/close
    display:none;         //mine, to make it expand and contract when opening/closing a branch
}