I suppose the easiest answer is you have to remember the people within the Guild. The death marshalls, (some of) the guild guard, the reporters, and the secretaries. The people who are doing what they do for the Guild because they think it's the right thing to do. As you've pointed out a few times, the other factions seem to be doing the right thing in the wrong way at times. The Guild, in my opinion, feels more like the wrong thing being done by the right people. I'd bet that every underling in the guild is there because the pay was good enough to support themselves and/or their family.
The Guild isn't meant to be sympathetic, it's people are