So I used GIMP, and created an additional layer on top of the original graphics that applied a HSV Hue over just the indicators. Then I just updated the secondary beacon tint so that it had the same RGB value.
I was a little annoyed, because the new beacon design makes running multiple colours impossible, or at least very hard. To be honest I haven't spent much time digging into to see if there is another way to do it, just gave up and went purple.