I don't think so...
The autolinking feature is, in fact, a feature of Moodle's core, not glossary's so the glossary module has (almost) nothing to do with the process itself.
If it is made to the glossary, it will has to be made to everything else, and it will affect other filters... I don't think this is the right path to go. It should be a redesign of the db, the process or, more probably, both (and it if it is ever done, it will be after 1.2 is released anyway).
By the way.. upgrading won't be difficult... will be extremely easy in fact... The hard work will be in re-coding your changes...
Perhaps you won't need them anymore, though.
Will