Well put and well thought out. Still, the key here is "some recruits." Not everyone is recruited, and while the nondiscrimination is 150 percent admirable, the anger of the others will not be mitigated by nondiscrimination. In the minds of some - emphasis on some - the anger will grow into a need to lash out, and who better to take it out on than the very people who put you in the situation. There are thousands of ways to get your pound of flesh from the Wardens, and in a feudal culture there is no likelihood that some of them will go down that very path. Moreover, as you say, "in some cases it might be an improvement over their old lives." Improvement however is subjective, and when it is not an improvement the anger will come out. Most particularly when you learn, recruit or conscript, that the first thing your new comrades did is to insure that you will die in agony and madness, possibly killing some of those very people that you care about. As noted elsewhere, the Wardens are an absolute power unto themselves and protected by plot armor. Needed or not, necessary or not, the Wardens are creating their own worst enemy. Bioware simply has not, to date, dealt with that issue, but a renegade Warden bent on payback as opposed to Anders who is bent on escape is not something the Wardens want to deal with. Nor has Bioware yet.
Those are good points, and I'm sure there will always be 'problematic' recruits among the Wardens, yet they are not enough to say that they are "creating their own worst enemy".
Armies around the world haven't imploded by forcing conscripted soldiers into their ranks. Conscription was for centuries one of the most normal ways of building armies, and history teaches us that the real danger didn't come from disgruntled troops in them, but from mercenary armies (not just 'armies composed by mercenaries', but the general sense of 'armies composed by professional soldiers who are there for the money') who didn't get paid on time. Normative social conformity is even higher in hierarchical structures. Sad as it may be, they also have ways to impose social conformity by force if need be. Discipline in any military corps is enforced, not suggested.
The setting provides a counter-example in the Circles. They conscript mages, take them away from their families and make them live in a world full of rules and regulations, they have to undergo secret and possibly deadly rituals, and they are always at risk of losing themselves and suffer a terrible death. Yet the mages tend to be more rebellious. Why? Check the differences: there is no clear, definite and positive goal ('be a mage' versus 'protecting the world from darkspawn'), there is a difference of castes between enforcers and enforced ('we are mages, they are templars' versus 'we are all Grey Wardens'), the public image that they could have of the organization before joining is radically different ('mages are responsible of the worst disasters in Thedas' versus 'Grey Wardens have saved the world several times') and there are different alternatives ('Mages in Tevinter, Rivain and the Dalish have it different' versus 'Grey Warden laws are universally acknowledged'). And yet, even in the worst case scenario, there have been mages opposed to rupture and DA:I always ends with at least some mages returning to the Circle system.
Legality isn't issue because grey wardens doesn't seem to actively pursuit deserters and you could live relatively normal lives Alistair spend 3 not very quiet years being drunkard in Kirkwall while Anders 7 years as healer in Kirkwall.In contrast to very hard life of grey warden it is much more convenient alternative.
Ah, but bear in mind that I didn't rule out the option of becoming a runaway (indeed, I mentioned Anders as an example of that), just that their return to their old lives would be impossible... which is actually Anders' and Drunk!Alistair's case.
Also, as you conveniently point out, those whose resentment is too high have a better chance at defecting and living as runaways than staging some kind of rebellion.