Is there any way to make a normal textarea in civi editable using CKEditor?
So we looked at how one of the existing CKEditor-enabled fields on the page was processed in the civi code base (we chose the footer_text slightly further up the Online Registration page) and tried to replicate the same processing with the confirm_email_text field.

Based on this, we changed two files.

1. civicrm/CRM/Core/I18n/SchemaStructure.php

In the original Civi code on our version this had the following settings for confirm_email_text: 

      'confirm_email_text' =&gt; array(
        'type' =&gt; "TextArea",
        'rows' =&gt; "4",
        'cols' =&gt; "50",
      ) ,


We changed this (it was around line 644) to:

      'confirm_email_text' =&gt; array(
        'type' =&gt; "RichTextEditor",
        'rows' =&gt; "4",
        'cols' =&gt; "50",
      ) ,


In other words, we changed the type from 'TextArea' to 'RichTextEditor'.

2. civicrm/CRM/Event/Form/ManageEvent/Registration.php

In the original Civi code on our version this had the following settings for confirm_email_text:

$form-&gt;add('textarea', 'confirm_email_text', ts('Text'), $attributes['confirm_email_text']);


We changed this (it was around line 423) to:

$form-&gt;add('wysiwyg', 'confirm_email_text', ts('Text'), $attributes['confirm_email_text']);


In other words, we changed the first argument from 'textarea' to 'wysiwyg'.

One more note

This code sufficed to display the CKEditor instead of the default textarea, and to save and retrieve the text that was written into it. However, during testing we found that our emails were not displaying images that had a src with a % sign in it properly. This was remedied by altering our Message Templates. They had the following line in them by default for including the custom confirmation text at the top of the confirmation email:

{$event.confirm_email_text|htmlize}


We simply removed the htmlize filter, so instead we had:

{$event.confirm_email_text}


This seemed to deal with the problem.

I should note that we removed the line of code mentioned in my original question from Registration.tpl before implementing the actual working solution above.