There is a way to do this.
First, make sure your "indent_guide_options" setting is set to only "draw_active":

"indent_guide_options": [ "draw_active" ]

Then, in your color scheme (I would recommend making a copy instead of modifying the original),
change the color of the guide to the same color as the background:

<key>name</key>
<string>Monokai</string>
<key>settings</key>
<array>
<dict>
<key>settings</key>
<dict>
<key>background</key>
<string>#000000</string>


<!-- color of line for current code block -->
<key>activeGuide</key>
<string>#9D550FB0</string>

<!-- the next two settings may need to be added to you color scheme.
I have them in my personal modified version of Monokai, 
but I can't remember where I got them -->

<!-- color of line for parents of current code block -->
<key>stackGuide</key>
<string>#000000</string>
<!--string>#51402FDD</string-->

<!-- color of line for siblings and children of current code block. 
Siblings & children only show if "draw_normal" is added 
to "indent_guide_options" -->
<key>guide</key>
<string>#303026EE</string> 

You are correct Mark, didn't think you could use two options but it looks like you can. Thanks!

I'm not seeing the described behavior in php or javascript.