Alignment doesn't exist as a concept in Iron Kingdoms
I think you actually need to remove the concept of an "alignment" from your campaign for the Iron Kingdoms setting. For starters, IKRPG doesn't have such a concept.
In addition, alignment doesn't really have a useful place it can be applied, even as a description. Khador, for instance, is largely a warmongering nation intent on expanding their borders. Are they evil? Maybe according to Cygnar, maybe not according to the Protectorate, and certainly not to themselves as they feel to have been wronged several centuries ago and are simply reclaiming what is rightfully their's. And look at Ios - the Retribution of Scyrah (an extremist sect within Ios) blames the decline of their deities on the human use of magic, and they have some strong circumstantial reasons to believe that. Does that make all human magic users evil? And Cygnar is plenty capable of acts that a typical person would consider evil, or at least "dark-grey".
And that's my point. There's no concept of an alignment other than what a citizen of the Iron Kingdoms might find offensive, and that will vary from nation to nation.
As for the Protectorate of Menoth, they're lawful as far as their faith is concerned (they follow the True Law and Menoth is often called The Lawgiver), and can be chaotic as far as Cygnar is concerned. But trying to define them as lawful/chaotic is burdensome and doesn't do the Menites justice. They're neither good nor evil and are easily capable of both good acts and evil acts. They're just different.
It's more about allegiances than good/evil
What you need to do instead is color your campaign with the faction your party will be allied to, rather than to an arbitrary alignment concept. The Protectorate is a religious extremist organization intent on shepherding humans back to devout worship of Menoth. Menities aren't evil, and are plenty capable of acts of kindness. They're simply zealous.
There are also some dedicated careers in the IKRPG for devout followers of Menoth, if they are so inclined, including a Priest of Menoth or Paladin of the Order of the Wall.
As for career restrictions, there probably shouldn't be any. The Protectorate works with mercenary forces, just as most other nations in the Iron Kingdoms do, which can include all sorts of races and careers. And loyal Protectorate forces certainly have their fair share of your typical infantry, support, and crafters. But some choices will certainly be better than others. A Priest of Morrow is probably going to be a poor idea. Since the Protectorate are pretty fanatical about their worship to Menoth, they don't particularly tolerate other human religions, especially followers of Morrow or the Devourer Wurm(1) who they consider to be directly competing with for the souls of man. I wouldn't restrict any careers, but there are definitely some that players could find problematic.
Before you start
I would spend some time reading more in-depth on the Protectorate of Menoth. Based on the direction of your question, it sounds like you might need some more information to really understand what they are about.
To start, re-read the fluff in the Core Rules and pay particularly close attention to the War of Souls (pages 12 and 26) that Menoth, Morrow, Thamar, and the Devourer Wurm are engaged in and the founding of the Protectorate (pages 45, 47, and 57). It probably wouldn't hurt to go through the book for anything pertaining to Menoth in general. Another good source of information is the Forces of WARMACHINE: Protectorate of Menoth book (particularly if you have a friend that plays the war game - you can ignore the model stats or use them as templates for some important NPCs) which will have more detail on the Protectorate with a lot of it in a first-person perspective.
Keep in mind that the Protectorate are absolutely fanatical about Menoth and effectively have access to the military might of a nation, but are also capable of picking their battles, can be reasoned with, and can be merciful if the situation warrants it.
As such, loyal citizens of the Protectorate will be striving to convert more of humanity to Menoth. They'll focus particularly on the membership of Morrow, which is the religion's largest competitor on Caen. There is also some effort in converting more of the tribal communities in the wilds, which often worship the Devourer Wurm, but not as much compared to the focus against Morrow. This naturally creates a lot of tension with Cygnar, where Morrow is the dominate religion after the Mentie pilgrimage to the Protectorate once it was formed after the Cygnarian civil war.
You can probably come up with some more interesting tips on your own if you dive more into the Protectorate's history.
(1): Circle of Orboros is often misconstrued by IK citizens as worshiping the Devourer Wurm. While the blackclad druids do derive their power from the world and thus from the Devourer Wurm, they actively work to prevent his return to Caen as it would be cataclysmic.