Separate mouse and trackpad settings with Karabiner
It seems that this answer along with its comments solves the problem using Karabiner. It's a bit complicated, so I'll post a full description here: 


Open Karabiner > Preferences
Go to the tab "Misc &amp; Uninstall" 
Click "Launch EventViewer"
In the viewer, go to the tab "Devices"


You should see a table with several columns including "Vendor ID", "Product ID" and "Device Name". 




Identify your USB mouse in the "Device Name" column, and write down the corresponding "Vendor ID" and "Product ID"
Go back to the Karabiner > Preference > Misc &amp; Uninstall and now click the button "Open private.xml"
This will open Finder where the file private.xml is, open it with your favourite text editor


Edit that file to look like this:

&lt;?xml version="1.0"?&gt;
&lt;root&gt;
    &lt;devicevendordef&gt;
        &lt;vendorname&gt;Apple&lt;/vendorname&gt;
        &lt;vendorid&gt;0x05ac&lt;/vendorid&gt;
    &lt;/devicevendordef&gt;
    &lt;deviceproductdef&gt;
        &lt;productname&gt;USBMouse&lt;/productname&gt;
        &lt;productid&gt;0x0304&lt;/productid&gt;
    &lt;/deviceproductdef&gt;
    &lt;item&gt;
        &lt;name&gt;USB Mouse Scroll Reverse&lt;/name&gt;
        &lt;identifier&gt;myUsbMouseScrollReverse&lt;/identifier&gt;
        &lt;device_only&gt;DeviceVendor::Apple, DeviceProduct::USBMouse&lt;/device_only&gt;
        &lt;autogen&gt;__FlipScrollWheel__ Option::FLIPSCROLLWHEEL_VERTICAL, Option::FLIPSCROLLWHEEL_HORIZONTAL&lt;/autogen&gt;
    &lt;/item&gt;
&lt;/root&gt;


Note that you should replace the fields vendorid and productid to the values you previously wrote down (from the EventViewer device list).


Save the file private.xml
Go back to the window Karabiner > Preferences and now select the tab "Change Keys"
Click the button on the top-right "Reload XML"
You should see a new entry in the table below with the name "USB Mouse Scroll Reverse" (or whatever name you set in the XML file)
Tick that box


That should be all!