The answer is no you cannot just drop in another version, it must be compiled against the specific version or else it would require some assembly mapping in Web.config
It is often problematic upgrading the Ajax toolkit, my add on products use it as does mojoPortal and the version used must be the same so whenever I update the toolkit I also have to make a new release of my products along with the new version of mojoPortal.
I would like to upgrade to the new version but when I look at the comments here it does not sound like a stable release and people are having problems with it. It has been my experience in the past that upgrading may fix some bugs and introduce new ones. It takes a lot of testing because sometime they break it so that it doesn't work in medium trust hosting and then I have to go back the previous version.
When I have time I will try upgrading it and testing to make sure it doesn't break anything but it is not my top priority so I'm not sure how soon I will get to it.