I'm thinking about runing this session and changing the bad guy in the end from Malefax to the Inquisitor than I made for the group.

Has anyone else done this and how'd it go?

My "Malefax" was a Knight of Ren with a frelling Narglatch... so yeah, go with it. Consensus seems to be that the Malefax encounter, as portrayed, can be a bit anticlimactic (so feel free to adjust it to suit your campaign, and the PCs involved).

While he lost the ancient sword, he did escape to fight another day (on the back of the Narglatch, of course).

What about using the temple as a base for my PC's? Or is that the idea of the mission? I only read a little of the second part of that mission, but it seems like that is how its setting you up.

The mission is basically ridding the temple of further dark side presence. Once completed, the temple could certainly be used to base further adventures.

I'm still using Whisper Base, from the AoR box set.