@LaurenLokker,
This is a very common question with a dissapointing answer.
consider first that in order for jquery scripts to work, jquery need to load. Now consider how cta's and forms work in hubspot, the scripts are called inline as the cta or form is loaded by the page. If jquery was loaded in the footer than your ctas and forms wouldn't work. This is actually pretty common with all content management systems. I think Hubspot runs a little fast and loose with script loading but for the most part they do what they can.
The parts of the page that you have found are not editable are located in the header and footer include tags that are required to create a page. If you have ever tried to publish a coded page without these include tokens then you will have seen the error about them beign required. They aren't editable because most all of what is pulled in by these tokens is required for hubspot to work so removing them would be detrimental to your sbuscription benefits.
You shouldn't need the cta or form script to load for each instance though and it looks like it is... that might be something to bring up with hubspot as I beleive that happens with everyone. You can swap cta modules/tokens for embed codes and strip the call to the script for all of them and maybe place it in the head or footer of your page but I haven't tested that so you would have to experiment.
I get hired to optimize hubspot sites all of the time and I can tell you that while you are being flagged for above the fold scripts it is usually the css and images that get you. Most sites are build using Hubspots default frame work css, and custom css is placed on top of that. Even worse, in alot of cases (usually with purchased templates) I have seen the default framework css under the evast theme css, under the purchased theme css, under the theme customization css. That is thousands of lines of unused or redundant css that gets loaded and read by the browser. Fixing it is a nightmare because you have to go through the css and transfer only what is needed into a new file.
Images are a monster resource hog to. I wrote a blog about this here. There are step by step instructions on how to fix a image as well. Bad images are an epedemic on the internet, Always optimize your images!
The best you can do to optimize your scripts is to keep a global script file that contains scripts needed for all pages, then page specific script files. don't dump all of your javascript into one global file because even if the script isn't relavant to the page it is still read and attempted to process.
It takes alot to optimize a site correctly and the best way to do it is as you build it. Going back after the fact is a nightmare. I make a living off of it but it is a nightmare. The only fault that Hubspot holds in this is that they make building a website deceptively easy so anyone can go in their and play developer without even being aware of the consequences. The errors you get are not Hubspot specific, you will get them with WordPress, Joomla, or any content management system when you template and content is properly optimized, and in situations where a script is required in the head or etc.
Here's a secret though: Google can't pass it's own page speed checker. go to any of googles thousands of pages and run it through the checker. I show this to cients all of the time.
Here's another secret: If you are using Hubspot then you aren't in the SEO game. Yes you should 100% optimize your site, and yes search engine rankings are always important, and your site should always load within a second at least, but you are in content marketing. You can get to the top of google with any free-ware cms or even with plain old coded files. If you paying for Hubspot you should be putting your efforts into creating awesome content, campaigns, and workflows. If I can't get a client focused on content over SERP then I put them in WordPress with Inbound Pro then pass them off to some old school SEO company.