According to the unofficial Dom3 Wiki, gems are only used to reduce spell fatigue to 50 or the lowest amount possible above 50.
See:
http://dom3.servegame.com/wiki/Gem_use
So, your Rudra must have been right on the cusp. Perhaps he would have used a gem had he more than 10 points of spell casting encumbrance.
To avoid the issue with an undesirable spell being substituted for a redundant bless, I would set the Rudra off in a corner by himself to ensure that the bless falls on him. That way, you can either put something you really want him to cast in the slot that had the second bless or script him to attack one battle turn sooner.