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I have some Grey Knight Terminators laying around and was thinking of allying them up and a Grey Knight Librarian with my Space Marines just for fun. How should I kit out the 5 man Terminators squad and Libby?

Well, that would really depend on the rest of your army.

Depends,

You definitly want a Psycannon on the Terminators, and one Daemon Hammer.

I like giving the rest Swords and rolling on Divination with my Librarian. He has about a 50% chance of rolling the psychic power that gives a 4+ invuln, and all the other powers are really useful.

The Librarian should have a Warding Stave and be Lvl3.

Psybolt are optional.

Why the swords? Aren't the Halberds better? I mean is the save in close combat better then killing them before they can swing at you?

I think that boils down to personal preference, and is also hard to analyze in this vacuum.

Swords add to resiliency, halberds add to killing power. Either are valid, though I suppose the argument could be made for halberds that you don;t need an improved invul if the eneemy is getting less attacks because you've already killed some of his models.

In general I think halberds are better.
With Grey Knight terminators you never want to be in CC with other armies' terminators. with that in mind, your terminators are going to rip through normal marines with ease, any weapons they have that can bypass your normal save are init 1.
so you dont really have to worry about high quality attacks, more about quantity. halberds really cut down the number of models that can attack you.
But again, personal preference