If you want to try a newer version of ajaxtoolkit with the current release of mojoPortal you could try deploy the newer dll and then setup assembly binding mapping in web.config. Though I'm not sure if it can work because there are problems in the way they did version numbers in ajaxtoolkit.
However, if you look at the closed issue about ajaxeditor not working in medium trust, it does not sound like they fixed it at all, they just say use the newer editor extender instead.
I ran into this problem several years ago and my solution at the time was to stop using the ajaxeditor. I was able to get our ckeditor control to work inside updatepanel so maybe it can work in popup extender.
If that doesn't work for you then use a normal TextBox and use HtmlEditorExtender from ajaxcontrol toolkit instead of using AjaxEditor. This was the solution I used in Form Wizard Pro when I ran into this problem with AjaxEditor not working in medium trust.
ajaxcontroltoolkit is a strong name signed assembly so we can't just go take the source code and re-compile it without breaking a lot of things because we can't sign the assembly with the microsoft key.
Upgrading to new versions of ajaxcontroltoolkit is tricky business so I cannot promise to try it myself soon. Problem is if I update it to a newer version in mojoPortal core then any other projects that also use it have to be re-compiled against the new version or try to use assembly mapping which as I said is problematic in this case due to the versioning of the toolkit where they ran out of numbers and now new versions appear older than old versions. So if I upgrade it in mojoPortal then I also have to upgrade it in Form Wizard Pro, Event Calendar Pro and other products and release those at the same time. But it may still break other people's projects and they may not be in a position to re-compile things they have running in their sites especially if they have some other 3rd party add on feature or custom feature but don't have the code available.
Myself I'm trying more and more to stop using the ajaxcontroltoolkit and just use jquery because ajaxcontroltoolkit is a mess and always problematic since day one. I've had many headaches from it in many versions of the toolkit. Almost every time that I have upgraded it I run into some new problem.