They sure sound like onion root maggots to me. The pupae are definitely visible and would do the exact type of damage you're describing.

If you have that much damage, I bet there were a lot of wild onions growing among the weeds. You may not have noticed them last fall, because they are usually dormant then. Onion root maggot pupae were no doubt already present when you planted. This is a rare disaster and I hope you are not too discouraged. I find that as long as I rotate onions religiously -- including the perpetual ones -- I rarely have a problem. In my experience, this pest ignores sites that have no living or rotting onion tissues present.

By the way, secondary organisms (fungi) enter the feeding wounds made by the maggots and cause extensive rotting.

Here is a link that might be useful: fact sheet on onion root maggot

To be honest I really don't think its onion root maggots. Like I said before, these little worms were unsegmented and not at all stubby in the shape of onion root maggots. There were no wild onions in this field beforehand - it was an unwatered, sparse field consisting of only a few grasses and bindweed.
It has been really wet here this year, and I am beginning to think it has something to do with that. The garlic leaves have started to become striped with yellow, which makes me think it might be some sort of disease (i.e. fusarium basal plate rot?) I think the little wormies might have been secondary feeders.
In any case, despite the yellowing and missing roots at the basal plate, the plants are looking large and pretty robust. Hopefully they survive and I can still get a good harvest.