It is also used as a replacement for garlic in dishes, for people who refuse garlic for religious reasons.
I've never heard of this. What religions ban garlic? (and pity for them, I love it!)
When taking out the entire plant, you also take out any organisms like bugs and such from their ecosystem, killing them in the process. Jains try and limit the amount of violence they cause (Ahimsa), so in turn they try and avoid eating rooted vegetables.
On top of this, by removing the whole plant you prevent them from sprouting again, which is effectively "killing" in Jainism.
All of this being said though, modern agriculture techniques kind of make this reasoning insignificant. Mass farming practices mean that all plants are effectively killed along with any organisms in that area when harvesting.
And to top it all off, many Jains do not follow this practice, at least in the US. Many of my family eat all of these things, maybe trying to avoid them during Paryushan (holy week).
Also, grow mixtures of plants together that naturally crowd out weeds, inhibit the spread of pests, and replenish certain nutrients like nitrogen. IMHO this is grossly under-studied but could become more relevant with smarter robotics.
Plants are hypercompetitive and constantly fighting for space and resources. The only reason modern agriculture works is we are so effective at killing weeds with machines and herbicide. Otherwise crop fields would quickly be taken over by whatever grows the fastest.
They may also adapt their diet to whatever is the most edible among the weeds. This year a grape vine mysteriously sprouted in my garden and started taking over before I realized what it was and murdered it to save the zucchinis. A Jain would probably be happy enough with the grapes. I had even considered adopting it.
Onions and garlic are thought to promote carnal thoughts and violate the "sattvik" food lifestyle.
Very interestingly, Kashmiri Hindus eat meat, but are forbidden onions or garlic.
At the time, I asked them about this and the reply was that onions and garlic are considered to be stimulants and spiritually bad for you. The following article further elaborates on this explanation (best consumed with a pinch of salt): http://www.krishna.com/domains/d6.krishna.com/why-no-garlic-...