I don't DM much, so it isn't something I thought too hard about ...
Hell, it only occurred to me to look up the text of Fast Healing right before I hit the post button (the bit about that line of text nearly ended up an edit instead of in the original post). My "house rule" was pretty much just my initial instinctual reaction.
Of course, to a degree, I'll tend to think more towards RAI rather than RAW in some cases, though. Vigor creating a "natural healing" effect seems a bit odd to me, particularly since it has a duration. Perhaps if it were an Instantaneous spell, in that it permanently changed your natural healing instead of temporarily giving you magic hp/round. I suppose if the writer of the spell wanted to make the distinction, he/she would've said "the target heals X hp per round" rather than "the target gets Fast Healing X". Or it's possible the writer didn't think about it that hard. No way to really know ...
And you're right, compared to the REAL craziness, this is kinda silly to worry over - but then, I'd want to curtail the real craziness too ...