That's because you have multiple dividers with the class "k-in". The selector you're using pulls all 5 of the "k-in" class elements then finds the closest element with a class of "k-top" (in each case this is their parent apart from the very last one), then removes them all.
If you want to specifically remove only one of those dividers you can give it a unique identifier and select on that:
<ul class="k-group" >
<li id="treeview_tv_active">
<div class="k-top">
<span class="k-state-selected k-in" id="k-in-3">Tasks = Modify</span>
</div>
<ul class="k-group">
<li class="k-item" >
<div class="k-top"> //I want to delete This DIV
<span class="k-in" id="k-in-4">Roles = User, Admin, Approver</span>
</div>
</li>
...
Calling:
$('#k-in-4').closest('.k-top').remove();