As for inserting scripts/css links in the page's head, you can include these in your ui function (for example inside fluidPage()):
tags$head(tags$script(src="[your source]")), # link to javascript
tags$head(tags$link(rel="stylesheet", type="text/css", href="[your source]")) # link to css
[your source] may be either an URL (like your case) or a relative path for an asset (either a JS or a CSS file, respectively) stored in your app's www directory. You can see example of this is a deployed app in
this article.
As for the part that requires you to add an instance of an object, you can either add your own script.js file to the www directory (see the app I linked to for an example) or explore the
shinyjs package to see if it can help you inject that directly in your app at the right time. You'll always need to know a little bit about JS in order to get something together. There's so seamless integration with that JS library in Shiny (like there is with the leaflet library, through the leaflet R package), so you'd have to be the one gluing things together.