Ilssac - not sure why you say this - but it is absolutely not correct. Coldfusion is a serverside application code and can pass coldfusion based variables into Javascript code which will be executed on the client side like all the other HTML related code.
Take
<cfset somevar = "##FF0000">
<cfoutput>
<script type="text/javascript">
$(function () {Highcharts.setOptions({
chart: {backgroundColor: {#somevar#....
This way you take your CF based content as a variable and pass it on to a javascript that runs on the client.