A few things.
Firstly, many of the antagonists in FF14 have justifiable arguments for their actions Heavensward is full of them.
One could argue both Nidhogg and the Archbishop were justified in there actions. Humans did cruelly and brutally betray the Dragons and this is after what the Allag did to them. The Archbishop was leading a people effectively damned to endless war due to something they were not responable for themselves.
However, the reasons they have don't excuse their actions. Foulques was wronged but his actions were also in the wrong. He took his anger out on all members of the Lancer's Guild rather than those responsible. Foulques is a tragic tale, something which the leader of the Lancer's Guild indicates. He was wronged. How he dealt with it though was also wrong. Its was a sad tale but sometimes sad tales happen. Lets remember that the Lancer's Guild leadership and members Foulques was wronged by don't seem to be the same as the ones there. Foulques was in jail for some time and after that spent more time obsessing over fearlessness before returning to the Guild. The current Guild Leader was a Wood Wailer till recently.
Also remember while wronged he did steal from the Guild which is what started it all. Add to that he targeted new lancers, not old ones and had contempt for those who didn't share his 'fearlessness'.
Secondly, Foulques failed in understanding one of the core lessons of being a lancer and sadly this is the core reason he ended the way he did. He mistook fearlessness with courage and risked peoples live trying to force this view on others. In the end it showed that his fearlessness wasn't fearlessness but denying his fear and as a result when things went wrong he crumbled.
Thirdly, you have different things at work here. There is xenophobia in Gridania. It is sadly one of the issues the city state has much like corruption in Ul'dah and the lawless underbelly of Limsa. This isn't universal and we see many times this attitude changing over time. The acceptance of Adventurers is a good example. The second point which I'd mention since you brought up the Ala Mhigan refugees is the people of Gridania have serious limits on what they can and cannot do. The reason they don't help the Ala Mhigan refugees isn't from cruelty or xenophobia but that the true owners of the forest, the Elementals, have decided that some of those who come to the twelveswood aren't acceptable to live there. Gridanians have to follow the will of the Elementals There is no choice there.
The Elementals aren't evil. They see the world differently though. The wellbeing of nature is first and foremost and the fact that people are trusted to live in the forest is only because Gridanians are willing to place the wellbeing of nature and the forest as important as their own.
Lastly there is a postmoogle quest which I think shows a alternative situation.
We see a pair of Keepers of the Moon who likewise are discriminated against to the point where one has ended up effectively doomed to live as a bandit due to the path survival took her down. When faced with her sisters despair and the xenophobia and frankly corruption of a group of Wood Wailers she decides there needs to be change. However she sates that she will do it by becoming a Wood Wailer herself and growing strong enough so that she can make sure neither those who her sister are now bound to or those who force her there can continue to do so.
Its an example of how we see someone faced with hardship and discrimination choosing to overcome and make things better rather than just lashing out vengefully.