Yep, you just have to define another mame exe in hyperspin for the older MAME version. Then for the games you want to use the older version, add an <exe> element in the mame XML list.
For example, in /HS/settings, make a copy of MAME.ini and call it MAME-oldVersion.ini. Open it up and change the path to the older MAME exe.
Then under /HS/Database, edit your MAME.xml file, locate the game to want to run the older MAME and add the following under that game:
<exe>MAME-oldVersion</exe>