The way I look at it, The Brotherhood doesn't care how its done. Just as long as its done. As I said before, if its easier to just buy it. That's fine with them. If you take it by force. They don't care either. Much like Dr. Li. If you can convince her to work on Prime of her own volition, cool. If you have to force her at gunpoint to do it. That's fine as well. Just so long as the jobs done.
At the same time though, clearly they aren't doing the Commonwealth farmers any favors. And presumably, sometimes they refuse to sell (my guess is you aren't the only one going around and extracting tribute). Either because they can't since they need the food themselves, or because they just don't want to hand it over. At which point The Brotherhood will probably just take it.
Doesn't make them evil. Its just normal operating procedure for occupying armies to feed themselves from the local populace. For the most part, that's how its been done throughout history. Brotherhood's no different.
So calling them evil for doing this isn't valid (IMO), but at the same time, faulting people for disagreeing with this levying of tribute isn't valid either.